The capacitors' purpose is two fold, to ease the draw and wear on your electrical system, and supply a quick and ready (and close proximity) burst of energy to your amps when you crank it, or when the base notes hit pulling big amps out of your power source. They store energy, and gradually pull their juice from your battery bank. You mentioned the big SOB batteries you have for the stereo. I would say that if your stock alternators can keep them charged, just try and stay with stock, otherwise you may overload your wiring from the alternators and battery switches to the batteries.
I took out my 2 factory batteries and replaced them with 2 blue-top Optimas in each's place, (4 total) wired in parallel.