The Habitation Deck is where crew and passengers live. It produces Sewage, which needs to be disposed of via a sewage system. For every nine squares of habitation, one cabin space is added. Habitation must be connected to the Main Deck with a Ladder to function.
The atmosphere passes into and out of the habitation deck via ladders. Walls built on the engineering deck extend into the habitation deck, meaning the habitation deck can be split into multiple atmospheres, so long as each section has a ladder for civilians to enter. Doors allow civilians to pass into other sections, but they seem to pass through the doors without activating them. If one section loses atmosphere, civilians will not automatically attempt to move to an adjacent section via a door. If they pass through a door to an adjacent section, the atmosphere does not equalize.