Galactica, as with other battlestars, has two flight pods: One port and one starboard. The flight pods contain the landing bays within the top and the hangar deck along with the launch tubes within the bottom half. Normally these two pods are extended so that the landing bays are open to space, but in order to perform a Jump, the pods must be retracted on a battlestar class such as Galactica's.
The port flight pod was the only flight pod on Galactica currently in use at the time of the Cylon Attack. The starboard flight pod's landing bay was converted into a pressurized museum of artifacts of the first Cylon War, including with a gift shop in the former launch bay. Crewman Socinus complains of the problems in keeping the landing bay's external windows sealed from leaks at the start of the Mini-Series.
The starboard landing bay remained closed off from space until a Cylon Heavy Raider later crashed through one of the windows, depressurizing the landing bay (Scattered).
Compartments within the flight pod can be sealed off frame by frame and vented to space to kill fires and prevent possible complete decompression and structural buckling. This occurred to the port flight pod after it was struck with a Cylon kiloton nuclear missile and was subjected to internal fires that threatened to ignite the ship fuel lines and destroy the ship (Mini-Series). The use of the busy port hangar deck as a morgue would be rather morbid, so Commander Adama orders Galen Tyrol to set up a temporary morgue be in "hangar bay B" after the loss of 85 crewmembers from the strike (Mini-Series). Since the port hangar deck (bay) is very busy with retrieving Vipers, and we see Captain Kelly with the bodies in what appears otherwise as an empty hangar deck, it is likely the unused hangar deck of the starboard flight pod.