I won't comment on the 6 volts.
However, I wouldn't run your system directly to the batteries. Amps have capacitance built-in, which will drain your batteries while sitting (even if the stereo and amps are off).
My solution? Two Perko switches and a big-ass alternator. With that, you can control what gets charged (or not charged) by the alternator, and you can turn everything off for storage.