Well, I'll leave the comments about a circuit city install to a minimum. Lets just say, I wouldn't be going there anytime soon (for purchase or install).
Could the Circuit city guys messed up the alternator? it's possible, but not probable. Alternators don't go by age or mileage, they go by luck. I think enough has been said to cover that.
Now onto my fav topic on this thread. Power issues. Batterys, caps, alts. Technically, Caps are indeed a joke. They do provide some extra power to cover for a few large hits, but they're not magic.
Rule #1: energy is conserved. Caps can't give off more energy than they take in. If you're listening to loud music, you're going to discharge the cap faster than the alt can recharge it. The goal is, when you're listening normally, the cap should be doing nothing, the alt should be producing enough power to charge the cap and run the speakers w/o needing help. Maybe a few big beats will come out that will be more than the alt can handle, therefore, the cap takes over for a second, then it's recharged as it sits idle. Oh, guess what, the battery does the same thing as a cap!!!! Get a deep cycle battery, it can do a better job than a cap, it has more capacity and voltage doesn't drop either.
Rule #2: only 1 source of power. Like I said, a cap or a batt cannot put out more than it takes in. You can get the most espensive cap you can find, you can get the most expensive battery you can find, hell, fill your trunk with them, I don't care, it'll actually hurt your alternator more than it'll help. The alt. has to charge everything up. If your cap can cover a bass hit, great, but the alternator has to fill the cap back up before it can take another bass hit.
Rule 3: here is what you need to do to get real results: It's called the big 3:
>Better grounding will allow the Alt. to run more efficiently and allow the battery to charge more efficiently, this will save the alternator's life.
>Better battery (deep cycle). Deep cycle batteries prevent voltage drops, They will continue to push out 12.5V for as long as possible. They work better than any cap and they hold more.
>Better alternator. Yes, you have a good bettery, yes you have good grounding, hell you may have a cap, but there's only one source of power, your alt. You need more power? Than you need a better source.