From Battlestar Wiki, the free, open content Battlestar Galactica encyclopedia and episode guide
When a Viper or Raptor returns to the landing bay from a mission, it is moved to one of several elevator platforms, which lowers the spacecraft down to an airlock and the hangar deck below.
Basic repairs, fueling and munition loading take place on the hangar deck. Other special space fighters, such as captured Cylon Raiders, Heavy Raiders, and the experimental Blackbird are stored away on the hangar deck as well. During Condition One alerts, pilots scramble to their fighters. For Viper flight, the deck crew pushes Vipers out into the launch tubes, which are accessible through doors on the hangar deck. Raptors are returned to the landing bay with the landing platforms for their launches; launch tubes are designed for use by Viper-class fighters only.
If a launch is aborted, the deck crew is called upon to pull the fighter out of the tube for quick repair.
During the First Cylon War, Galactica was outfitted with additional hanger racks in the bays, effectively creating a Viper storage and servicing level above the hanger deck, and allowing her to carry up to triple the amount of Vipers compared to her post war configuration (additional floor space free by racks can be utilized to store Raptors).
Currently, only Galactica's port hangar deck is available for flight operations. The starboard hangar deck is largely empty as the whole flight pod was to become a museum on the battlestar's scheduled decommissioning (Miniseries).
Launching spacecraft there is problematic since many of its facilities were stripped for the expected museum. The expanse of the empty starboard hangar deck has been used as a temporary morgue as well as an assembly hall for speeches to the crew at large. After the exodus from New Caprica a refugee camp and a bar are established there.