It never ceases to amaze me just how little most audio guys know about how an alternator and battery system works, lol. As far as the alternator is concerned, two batteries in parallel looks like one big battery with slightly lower internal resistance. In no way does this make the alternator work any harder. All the second battery does is provide a larger buffer between the alternator/"main" battery than a cap would. As I've said before, if you listen to it cranked ALL the time, the second battery will eventually give out. But for "normal" listening, where there are periods of time where the car is driven without the stereo causing permanent hearing loss, the backup has a chance to recover and everything catches up.
Rewiring or upgrading the alternator is ABSOLUTELY the best way to go. If you can't afford an alt - and they're getting cheaper all the time - a second battery is a better option than a cap is.
