Auxiliary control (or the Auxiliary Control Center) was a key section of Federation starships in the 23rd and 24th centuries, and acted as supplemental control centers to the bridge and main engineering. If the situation warranted it, the starship could be completely run from auxiliary control.
During the lead up to the attack on the Levaeri V station by the USS Enterprise and the Bloodwing in 2275, it was necessary for Commander Ael to pretend that she had captured the Enterprise so that the starship could enter Romulan space. While a team from the Bloodwing occupied the bridge, Captain James T. Kirk and his crew continued to run the ship from auxiliary control. (TOS novel: My Enemy, My Ally)