There isn't one Heaven. Each soul generates its own paradise.
God resided in Heaven with his angels until his departure sometime in the distant past. In God's absence, the archangel Michael led the angelic Host and directed the affairs of Heaven. Raphael was also an authority. The appearance of angels in Heaven is not necessarily human, even though they may be perceived in that manner by deceased souls. For example, Zachariah says that in Heaven he has six wings and four faces. Angels draw some of their powers - demonic exorcism, healing and possibly resurrection - from Heaven. Those who fall and are "cut-off" from Heaven are weakened, and are not allowed to return on their own. It is still possible for the banished to communicate with Heaven. Anna and Castiel were able hear other angels speaking, even without their grace. Castiel is able to communicate with Sam and Dean through a link to electronic equipment - such as a radio or TV - in their memories.
Heaven also serves as a destination for deserving human souls after death. They occupy the happy memories they experienced on Earth, reliving them in their personal Heavens. It is unknown how a human soul is allowed salvation in Heaven. Joshua suggests that it is on a case-by-case basis and can be God's decision; this is the case with Sam and Dean. Raphael says that if a person is devout, it can cover all sins when Castiel questions Ken Lay's admittance into Heaven.
Following Michael's and Lucifer's imprisonment in the Cage, civil war raged between Raphael and his angels against Castiel and his angels. This civil war had ended when Castiel killed Raphael along with his followers after absorbing the souls from Purgatory and declaring himself the new "God." The aftermath caused the number of angels to dwindle significantly.
Angelic society in Heaven is arranged into a rigid, militaristic hierarchy. Each angel is a member of an angel garrison with its own supervisors who report to higher authorities. This arrangement has been breaking down since God's departure from Heaven. Following the imprisonment of Michael in Lucifer's Cage, Castiel describes the situation there as civil war. Garrisons now seem to be breaking up due to the conflict in Heaven. After civil war ended, and Castiel disappeared, there was a void in the leadership of Heaven; though angels still appeared to have a hierarchy, there were many factions vying for control. One of the leaders of those factions was Naomi, who held an unknown rank, but was in charge of Heaven's Intelligence Division. After the angel fall, and second angelic civil war on Earth, the remaining angels formed a quorum to govern, with the angel Hannah as a high-ranking member.
It’s called the Axis Mundi. It’s a path that runs through Heaven. Different people see it as different things. For you, it’s two-lane asphalt. The road will lead you to the Garden. You’ll find Joshua there. And Joshua… can take us to God. The Garden. Quick. Hurry.
The Axis Mundi is a path that runs through Heaven. Different souls in Heaven see it as different things -- for Dean it is "two-lane asphalt." According to Castiel, some view this axis as a river. The road will lead the traveler to the Garden.
In mythology the Axis Mundi is the path between Heaven and Earth, and is depicted symbolically in different ways in different cultures -- from the Totem pole of American indigenous people to the Pyramids of Egypt and the Bodhi tree where Buddha found enlightenment (Source).
See, you gotta stop thinking of Heaven as one place. It’s more like a butt-load of places all crammed together. Like Disneyland except without all the anti-Semitism.
In Heaven, humans occupy their happy memories, reliving them in their own, separate worlds. When Sam and Dean are killed and find themselves in Heaven, they move along the axis mundi from one happy memory to another -- although the memories that are happy for one brother are not always so for the other. When they meet Ash, he explains that everyone has their own “Heaven,” and at the center of all of them is Heaven's Garden (see below).
According to Ash, most people cannot leave their own “Heaven,” although Ash had worked out a way to do so using his practical application for string theory, he has also rigged a device that allows him to listen in to the angels. Other people Ash has met in Heaven are Johnny Cash, Andre the Giant, Einstein, Pamela Barnes and Mallanāga Vātsyāyana who wrote the Kama Sutra. Ash tells Sam and Dean that he has been unable to locate John or Mary Winchester.
Ash also tells Sam and Dean that some people (Ash referred to these people as "special cases" because of the rarity), for example, soul mates share their Heaven with each other. Ash suggests that Sam and Dean share the same "Heaven," given that he encountered them together.
Angels have access to people's personal Heavens. Zachariah appeared in Dean and Sam's memories, and Adam informs Dean and Sam that the angels recruited him while he was experiencing a happy memory in Heaven. Charlie described her brief time in Heaven to Dorothy as Christmas day with her parents.
When Bobby was asked by Sam and Castiel to break out his Heaven to open a portal to Heaven for Cas, it is shown that all the personal Heavens are organized alphabetically by name and numerically by year, as evidenced by Bobby seeing the names of various Robert Singer's (and Roberta Singer) that have lived and died throughout time. When one faction of them escapes, one angel exclaims "The Bobbys are fighting back. All hands, we need all hands. They're surly, I repeat the Bobbys are surly.".
Angels can choose to spend time in the personal Heavens for their own reasons. Castiel enjoys an autistic man's "eternal Tuesday afternoon" Heaven, which is a peaceful park scene, and Raphael uses Ken Lay's Heaven for meetings.
According to Ash, this garden is the core of Heaven, and is at its center. This portion of Heaven, according to Joshua, can be referred to as God's Throne Room or as Eden. Joshua is an angel who tends the Garden. Souls that travel to the garden, according to Joshua, will see it differently; for Sam and Dean, it is the Cleveland Botanical Gardens that they visited on a grade-school field trip.
The angel Gadreel was chosen to protect the Garden and keep evil from entering it. Gadreel somehow failed in his task and allowed the Earth to be cursed with evil for which he was blamed and locked up for thousands of years in Heaven's darkest dungeon.
Virgil watched and protected the angelic weapons before the angelic civil war. During the chaos after Michael's imprisonment, numerous powerful angelic artifacts were stolen by Balthazar, including the Staff of Moses and Lot's Salt.
Naomi would hold regular "debriefings" with Castiel as well as other angels in her personal office, which had a very cold and sterile appearance to it. It's in this office that Naomi would go about brainwashing other angels, whether it was to perform a specific task or to erase their memories of any missions they were sent on. For example Castiel not being aware that he took part in the slaughter of the first born sons on Egypt when the ten Plagues of Egypt were unleashed.
In 9.18 Meta Fiction, Metatron takes Castiel to his office after he is captured and implants an illusion in his head of Gabriel asking him to lead an angel army against him to make Castiel the "villain" in his story. He offers to give Castiel a new supply of grace in exchange, but he refuses. Their meeting is cut short when Ingrid arrives with news that Gadreel has been captured by the Winchesters. After everything is over, Gadreel and Metatron meet in his office to discuss what happened and Metatron then goes back to typing up his version of everything that happened.
In 9.22 Stairway to Heaven, Metatron and Gadreel talk in his office before they go to meet with Tyrus. Metatron later communicates with Castiel and his followers through a web cam from his office and is pleased when his efforts to bring them to his side with suicide bombers work. After Metatron gets a call from one of Castiel's former followers, Gadreel confronts him over this and it causes him to leave Metatron to help Castiel and the Winchesters.
In 9.23 Do You Believe in Miracles?, Neil helps Metatron make a broadcast on angel radio using a device in his office and he then leaves for Earth to convert humanity into following him instead of God. Gadreel and Castiel try to infiltrate Heaven to break the angel tablet and help Dean stop Metatron, but are tricked into thinking they are in Metatron's office only to be locked up in Heaven's prison. After Gadreel sacrifices himself to release Castiel, Castiel searches the office and eventually finds the angel tablet in the typewriter. After Castiel breaks the tablet and Sam swings at him with an angel blade, the now-vulnerable Metatron flees to his office where he finds Castiel sitting in his chair. Metatron binds Castiel to the chair with handcuffs and then taunts him how the angels won't believe the truth and Dean is dead. Before Metatron can kill Castiel, Castiel reveals he had switched on the broadcasting device in the office and all the angels are listening in. The angels storm the office and overpower Metatron and release Castiel. However, rather than use the opportunity to kill Metatron, Castiel imprisons him in Heaven's dungeon.
Dean: Where have you been?
Anna: Prison. Upstairs. All the torture, twice the self-righteousness.
Heaven also appears to have it's own prison/dungeon where angels are held and tortured for disobeying orders. Anna is taken there during 4.21 When the Levee Breaks and reappears in 5.13 The Song Remains the Same claiming to have escaped, though Castiel tells her no one escapes from Heaven's prison, saying if she got out, it was because she was let out to do Heaven's dirty work.
The angel Gadreel was also an occupant, having been locked-up for thousands of years in Heaven's darkest dungeon for having failed in his duty to protect the Garden from evil entering and cursing the Earth. Metatron also reveals to him that all the angels in Heaven, even the imprisoned ones were cast out to Earth by his spell explaining as to why he was released.
In 9.23 Do You Believe in Miracles? Castiel and Gadreel are imprisoned in Heaven after the angels Hannah and Ingrid see through their ruse of Castiel being captured. Castiel is able to escape the prison after Gadreel sacrifices himself, which causes the cells to be destroyed. Castiel later locks Metatron in an intact cell rather than killing him.
In 10.01 Black, Hannah reveals that Metatron's cell door has been made permanent. In 10.02 Reichenbach, Hannah visits Metatron in the still-damaged prison where he is now in a straight-jacket and he offers to give her the remainder of Castiel's grace if she releases him. However, Castiel stops her and Metatron remains locked up.
In 10.17 Inside Man, Sam and Castiel make their way to Heaven's Gate to release Metatron to find a cure for the Mark of Cain, but Hannah is reluctant to release him. After making contact with Bobby through the psychic; Oliver Pryce, Castiel is able to make his way back into Heaven and reach Metatron's cell alongside Bobby. Castiel releases him and removes his grace, rendering him mortal and susceptible to gunshots. Although Metatron doesn't know how to remove the Mark, he agrees to take Castiel to the location of the remainder of his grace.
Internal conflicts have raged in Heaven during periods of intense strife, which led to what is known as the Angelic Civil Wars, conflicts that were fought in Heaven and on Earth between the Host of Heaven. The first known Angelic Civil War was a product of the aftermath of Lucifer being re-imprisoned along with Michael during the Apocalypse. The archangel Raphael attempted to restart the Apocalypse by breaking more seals and releasing his brothers from the Cage, but the newly resurrected and upgraded seraph Castiel stood in opposition to Raphael's plans, and in an act of defiance rebelled against Raphael's rule, igniting a war that would rage for two years between the Holy Host of Heaven.
The Second Angelic Civil War was a product of the Fall, with all the angels having been ejected from Heaven, a power vacuum formed with various factions of angels seeking to lead.
First Angelic Civil War
Soon after the defeat of Lucifer and Michael, Castiel's return to Heaven as a new leader brought consternation from the remaining archangel Raphael, who saw what Castiel did as rebelling against God and Heaven and intended to have Castiel pledge his allegiance to Raphael in front of the entire Host of Heaven before releasing Lucifer and Michael from the Cage. When Castiel refused, Raphael displayed his power and ordered him kneel before him or he and any angel that follows him will die.
In his desperation, Castiel begins a partnership with the newly crowned King of Hell, Crowley, to find Purgatory and divvy up the monster souls between them, with a good will gift of 50,000 damned souls from Crowley, Castiel confronts Raphael in Heaven, where he declares his intention to go to war and claiming there will be no Apocalypse, before telling the angels to choose a side.
In an early incursion, Castiel led a small force of twenty angels behind enemy lines to victory against Raphael and his loyalists. News of his victory appeared to galvanize many angels into the cause, giving Castiel a reputation as a great leader. For two years Castiel would battle against Raphael, while working with Crowley to locate Purgatory.
Upon gaining the ritual to open a doorway to Purgatory from Dr. Eleanor Visyak, Castiel betrays Crowley intending to give him none of the souls, offering Crowley two choices, "flee or die." Scoffing at Castiel breaking their deal, Crowley flees, only to return sometime later with Raphael, having formed a new partnership with the archangel. Giving Castiel the same choice to hand over the blood for the ritual and to "flee or die", Castiel leaves the blood and teleports away. Crowley performed the ritual, to no effect, until Castiel appeared once more revealing the blood he gave Crowley was dog's blood and has taken in the souls of Purgatory himself, showing his new power by filling the room with a bright blinding light. As Crowley makes his escape, Raphael is unable to teleport due to Castiel's new god-like powers. As Raphael begs for his life, Castiel snaps his fingers, causing Raphael to explode at a subatomic level, killing him. Declaring himself the new "God", Castiel makes his first stop in Heaven, where he slaughters Raphael's loyalists, ending the war before turning his attention to Earth.
Second Angelic Civil War
After the Fall, many angels became desperate for vessels, and would take or attempt to take any human that would consent. This need for "housing" would eventually give rise to various factions forming, who would use their power to find suitable vessels for angels in need. Three known factions were lead by Bartholomew, Malachi and Tyrus. Bartholomew and Malachi would eventually go to war with each other over Bartholomew's refusal to work with Malachi's faction in getting back to Heaven. A peaceful faction of angels known as the "Penitents", angels who sought to live humbly among the humans, would also become targets of Bartholomew, who would kill their leader Rebecca out of fear they would become a threat down the line. As Bartholomew consolidated his power, he also sought out Castiel, offering him a place at his side to locate Metatron and take back Heaven. Castiel, however refuses his offer after being ordered to kill a Penitent angel, and turns the blade on Bartholomew, and kills him.
Soon after the death of Bartholomew, Metatron begins recruiting angels to join him in Heaven. Sending out Gadreel, who uses the Horn of Gabriel to call angels to him, he makes offers to the gathered angels to return to Heaven, killing those who refuse. As Metatron consolidates power through Gadreel killing the opposition, of which included Malachi, Castiel is chosen by Metatron to be the villain to his hero. Telling Castiel to lead the rebels to their deaths, and he will have a place for him in Heaven. Castiel refuses to follow Metatron's script, instead galvanizing as many angels as he can on Earth, to legitmatly take the fight to Metatron.