^^ I'm vague on this, but were there ever any references onscreen regarding where Auxiliary Control might be? Could you have two Auxiliary Control rooms, one in the saucer and one in the support hull? And Auxiliary Control is certainly something that could be depicted in more detail in the tech manual.
From "I, Mudd" for the Enterprise:
KIRK: Intruder alert, deck eight, auxiliary control.
Dialogue from other episodes seems to point to only one aux control but like the "one" transporter room, it could be just a matter of which one is active at the time of the episode if you want to interpret as two control rooms.