I would reccomend disconnecting the battery on the 12 Volt vehicle to avoid any possibility of a voltage spike damaging the alternator or the computer. Of course, if it's an old-school rig with a generator and a point-type distributor that just happens to be 12 volt, no problem. Don't make any sparks around the top of the hot battery, as that's inviting a hydrogen explosion. Get the cables attached to the top of the 12 volt battery first, then attach the + cable to the top starter connection, then put the - cable somewhere that's a good ground like the generator bracket, etc. You'll get some pretty nasty sparks as the ground is connected because the 12 volt battery is going to start fast-charging the 6V immediately. Don't stay hooked up for long!
Jerry