If your total system power is 1000 watts RMS or more, you will need to:
1. Upgrade the alternator to a high output alternator
2. Upgrade to a heavy duty deep cycle battery
3. Upgrade the "Big 3" - that is to replace (or add to) the power wire between the battery and alternator, the ground from the battery to the chassis and the ground strap from the engine/tranny to the chassis with at least 1/0 AWG wire.
Failure to do this will result in you replacing them anyway as the alternator will eventually fail.
Here is a guide that will calculate what size alternator and power wires you need http://www.datafilehost.com/download.php?file=6d26c621
A second battery is never a good idea as it's an added strain on the alternator to charge two batteries AND supply power for the car. The ONLY time a second battery is useful is if the audio system is to be used with the car off.
A cap is only good so far as the audio system isn't trying to pull too much from the electrical system. A cap doesn't provide more power, it's designed to 'stiffen' the voltage to the amp, nothing esle. If the current isn't there, a cap won't help. The alternator must have at least 20% more amperage power than the entire vehicle and sound system combined for a cap to be of benefit which is ironically the same requirements for an amp to be efficient.