i think that for charging a battery you need a special module that makes the voltage about a constant 13 volts or something, so that at idle youre not putting 6v into the 12v battery.
the headlight on the baja is 12 volts because when i added my battery the headlight was very bright since it was getting 13.5 volts directly from it.
also i am curious to know where you are planning to put a battery and what kind. on mine i swapped out the clone for a tecumseh HM100 10HP. comet 30, and AGM sealed battery.
i went the route for the AGM (glass mat) powersport battery because it can withstand vibrations, its small, light, and can be mounted at any angle without spill. so if i crashed the bike the battery will not leak. but it was $90 at Napa.