I have 2 batteries in my Contour, and the one in the trunk definitely helps, BUT it will only give more reserve until your batteries eventually get low and alternator must provide. You say that your alternator is 'high output'. But to me, that says nothing. How much higher output is it? 10 amps above stock, 20 amps, 30, 40, 50? Do you even know what a stock one runs at? I've known on all my old cars, but I don't even know what the stock Contour's alternator is rated at, because this system I got now is the most suttle I've ever had (I'm 30 now, and sound volume is not as important as when I was younger). But it's all just about laws of physics dude. You need to calculate the amperage draw of your amps at full volume (highest you normal would listen to it at) first. You can check amperage by using inductive amp draw probe (many shops have these), and if you are drawing say, 40 more amps than stock, then you should upgrade your alternator to have 40 amps more rated output than a stock one would push. And this is expensive. You could spend $500 on a stinkin alternator for cryin out loud! But on an old Mustang I used to have that had 4 amps in it, instead of buying one of those high dollar Phoenix Gold alternators, I instead just bought a STOCK alternator for a Lincoln Continental with every option (more amps), and I had to weld up and fabricate my own new brackets so it would fit my car (because it was physically bigger and didn't fit old brackets), but after that I had all the power that I needed. But really, this is the CORRECT way to fix your problem.
Other simple things you can try to preserve your factory alternator's lives may include:
1. When you have stereo cranked, turn down heater fan to low, turn windshield wiper off or to lowest needed setting, and in general, just try to turn anything off that you don't REALLY NEED, like foglights, etc.
2. When pulling up to stoplights, or just sitting there idling engine, then REMEMBER that alternator output is cut in HALF of it's rated output at idle, so at idle: turn you heater fan lower, don't use your power windows and other accessories too much, and turn your stereo down just a tad, so it's not maxing out the current draw at idle. This will help your batteries to not discharge as much, meaning that alternator wont have to work double and get so hot once you pick up the RPMs again.
I practice these techniques with my stock alternator (my stereo system is JUST barely pushing the borderline of needing a higher current alternator), but I have no, and have never had any problems with mine. I'm still running the original alternator after 110,000 mi.
