Is this a multi site or simulcast system? Multi site would seem to be more oriented to having different talk groups 'affiliated' with a given CC. Simulcast everybody is retransmitted, so it really is kind of a mute point. You could be out of range of the CC you have for a TG you want to listen to.
Though that really probably doesn't matter. You could try programming each control channel into a different bank on your 96 and put the TGIDs you want for a specific CC into that bank. Just make sure the bank is closed so it won't stop on any TG that is being broadcast.