Auxiliary Fire Control is located in the forward section of a Colonial Battlestar. This area likely allows the battlestar's gun batteries or missile launchers to be fired in the event that CIC cannot control these functions or if the command crew is incapacitated.
Cylon Centurion forces infiltrating battlestars are reputed to use a tactic wherein their boarding parties take control of Auxiliary Fire Control, as well as Aft Damage Control. The Cylons in Aft Damage Control (which is able to coordinate bulkheads, vents, and firefighting throughout the ship) will attempt to vent the ship's atmosphere into space, asphyxiating the crew. Then, with no further hindrance, the Cylons in Auxiliary Fire Control would turn a battlestar's gun batteries at other Colonial ships to destroy them.