Auxiliary Fire Control is located in the forward section of Galactica. 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.
Colonel Saul Tigh recalls this tactic while Galactica is boarded by advanced Centurion models, delivered by a Heavy Raider that managed to crash-land in the starboard flight pod landing bay during Galactica's battle with a basestar (TRS: "Scattered").
Tigh learns of this ploy from William Adama, as he recalled a similar attempt by Cylons that invaded Galactica while he was stationed there in the last week of the Cylon War some 40 years earlier (deleted scene, "Valley of Darkness").
To combat the Cylons, Tigh (in command of Galactica after Commander Adama is shot by Sharon Valerii) orders teams to stop the boarders from reaching these key control areas at all costs. A team, led by Sergeant Hadrian, is successful in defending Auxiliary Fire Control (TRS: "Valley of Darkness").