[MrForbes]

If you connect the two batteries in parallel, you get twice the current available. If you connect them in series, you get twice the voltage. For the FRC electronics, twice the voltage would be a bad thing, as the system is designed to run on 12v (nominal).

What kind of extra stuff do you have on the robot that concerns you?

Have you considered replacing the normal FRC battery with a car battery? It would have about 4 times the "reserve capacity", so you wouldn't need to charge it as often.