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.
Following Michael's imprisonment and Lucifer's re-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. 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.
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 or few 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 may 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. 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.
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.
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, as an explanation 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 capture. Castiel is able to escape the prison, after Gadreel sacrifices himself, which causes the cells to be destroyed.