Generally with Gestalt, you just choose your Gestalt class as your FC so that you get the bonus every level. The only time you would not want to do this, is if you happen to want to get an optional racial/class FC bonus from a class other than your gestalt. For instance, extra spells for a sorcerer which is not your gestalt class.
After a long day of very little sleep and entertaining my cousin, her fiance, and her newborn, I'm about to cash in for the night.