A 12 volt battery is just four 1 1/2 volt cells connected together in series internally. So a 6 volt is three 1 1/2 volt cells connected together.
If you put your two 6 volt batteries together in series you have a 12 volt battery in two parts. So charging them in this configuration is just like charging a 12 volt battery.
When I was a kid (we did stupid things back then) I would take and punch a nail in the top of an old car battery between the cells. If you hit the plates right you'd get various voltages. Connecting wires to one post and each of the nails you could get 1.5, 3, 6, 7.5, 9, 10.5, and 12 volts for projects that required various voltages.
I wouldn't recommend this though. Danger of explosion.

Conform and be dull.