There's some incorrect information here..
The rule of thumb for the size of capacitor is, 1 Farad per 1000watts RMS..
If you're running two 1000w amps, on a stock honda charging system, without a capacitor, then without trying to insult, you're running shitty amps, or very low-end equipment.. (Pyramid, Optimus, Rockwood, etc)..
Put two 1000w JLAs or something on that stock alternator and see what happens....
A Capacitor stores energy.. When a bass note hits, the amplifier need voltage right away, and alot of it.. So it takes it from the stored capacitor energy, rather than knocking the hell out of your alternator and battery to get it.. And since a capacitor charges quite quickly, it's usually ready for the next beat..
Using capacitors, I've used 4 Orion 1000w amps in a '73 Beetle, pushing 4 18" subs, all off the 40amp Alternator, with no ill effects, and without killing the alternator is short order..
There's much more to look at than just wattage of the amp and what your alternator puts out..