Some of my friends /competitors run two batteries in front of their feet so if you install a 1/4 aluminum plate up there you could probably bolt them down I think bolting one in front and one in back sounds problematic and I have never seen someone mount two behind the rear axel but with 80-100 pounds of weight back there I'll bet it does cool wheelies
I have no experience with Rock or Braile batteries but I have seen a 12V fan smoke when we hooked up the 16 volt battery charger to my friends car and I notced that when the 16 volt sttuff goes dead it seems to do it all at once.
So if your driving the car back I think an alternator is a good way to keep everything happy including your MSD box.
Good luck