Caps are generally frowned upon because they can only charge up to the same voltage that the battery is charged to by the alternator. Usually the alternator becomes the weak link in the system because during long bass passages it can't maintain it's regulated voltage (usually 13.8~14.4v) at the battery and thus at the Cap and amplifiers once the Cap discharges. Especially when your stock 75~125A amplifier is trying to compete with your vehicles integrated electronics are drawing roughly 75% of that amperage. That only leaves the remaining 25% of that amperage to try and maintain the voltage at your charging system, and car stereo, all while your amps are trying to draw 50+ Amps . Plus, whatever energy the Cap does store, it is discharged as soon as the voltage across it starts to drop. And then it must recharge, and at that point it just becomes an unnecessary load to your alternator. I know that was pretty simplified but you get the drift.
Now does that mean that a cap can't be beneficial? No. A Cap can still be usefull in smoothing the voltage supply to the device it is connected across, ie. your amps. It is the very same reason your amps own internal power supply has those huge caps, to stiffin and filter the rail voltage from sagging. During those long bass passages we've allready determined that it can't stand up very well; but, at normal listening levels, the cap can help smooth out the major dips in your amps supply voltage that normally would have been present at those peak transients, saving on the rest of your charging system. Which is why you can see your lights dim less frequently. The more capacitance you have connected across your amp, the smoother that voltage delivery will be.
So in your case, since you've allready got the cap you might as well use it. It can't hurt. But I hate to see people spend a ton of money on multiple caps, or 25+ farad caps becuase if they are that serious about their system, then they should just spend the money on an HO alternator and upgrade their big 3 cables.
I hope that wasn't to long, or to over simplified.
