you may want to invest in a second battery setup if you think the system is putting that much strain on your alternator. most likely, you aren't hurting anything, at least not that much, but you have to expect a little wear and tear when you have that much extra power.
and what're you running? 2000 watts, RMS? peak? is that just what the box said? sorry, I'm not trying to make you out to be an audio dummy or anything, but usually those with really expensive/top of the line systems know a thing or two about car audio, and capacitors are pretty basic.
