Are you talking about running an alternator for the 12V and keeping the generator for the 6V system? That would work if you could figure how to mount it but probably un-necessary.
If all you are running off the 12V battery is a stereo it will take a lot of running to run it down. Rig a power outlet for it and plug a trickle charger into it every night.
As far as starting better on 12 V, if you have proper size cables and good proper grounds you will have no problems starting with 6V.
