On my TT I have two 12V batteries that I've connected to one of these:
A marine type battery selector/switch which allows me to disconnect EACH battery. I can also connect one or both, depending on whether I want to insure I have reserve power (by using one at a time).
Switch is less than $50 and can be installed using some pre-made battery cables from your favorite Auto Parts Store. I chose to buy #4 awg Welding Cable, terminals, and a crimping tool. Revamped my entire 12V power feed with larger wire.
If you have two 6V's in series just use the switch from Blue Sea Systems that's an off/on rather than 2 battery selector/on-off.
I would not leave two 12V batteries connected in parallel for storage unless on a battery maintainer. One bad/weak cell can drain both.