Capacitors do nothing to help your issue.
The most important upgrade for very high power stereo systems is the alternator. You need a high output alternator, that alone will make a world of difference. With really high power set-ups your drawing more AVERAGE power then your alternator is designed to handle. This ultimately destroys the car like you mentioned.
Others have made good suggestions, your best bet is to upgrade your entire electrical sy stem. High output alternator, a very good battery, maybe two. Also upgrade all your wiring with a larger diameter wire.
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