charging a pair of batteries in parallel

Batteries in separate compartments are such a rotten solution. Like Scott just said above, these discussions usually turn more complicated. In the long run, all batteries have a certain number of charge/discharge cycles before they are done. The problem with 2 12 volts in series (and the good thing about 2 6 volts are in parallel) is with 12s, since no 2 batteries are exactly the same, the better 12 volt will always be attempting to charge the weaker one and when the charger is on, it will always be charging the weaker one while overcharging the stronger one. If you look around, most people get less than 5 years out of 2 12s but most 6 volts last about 7 years. The 6 volts in series don't have the self-discharge situation of 2 12s in parallel. Not a reason to just swap out batteries but when it comes time to replace the 12s, you will get more value out of switching to 6s. The separate compartment situation does make that a challenge, though.