YOu are all hitting on the right spots first off whats the amperage on the fuses on the amp ill tell you exactly what that amp is putting out. Im guessing its a class D amplifier. The first things you need to do is clean up your engine bay and that means all of your grounds. This will take some noise and add better current for your alternator and amp. Basically what Banging Jimmy said, Ground battery better, Ground alternator better, Run lead wire from alternator to battery with big awg wire. And Ground your motor. Thats what causes alot of humming or vibration in the music. Basically this should cost you around 20$ to do. EZ and simple.

Next Yes caps are ok, but they put more strain on your battery and alternator then anything. So i would recommend not using one of these. Since you only trying to run under 1000 watts. Which i know that amp isnt pushing 1000 watts All you really need is a good Deep Cycle battery and some good wire. I prefer Tsunami or Yellow Tops. You dont need more then 1 battery. You could upgrade the alternator, But are you made of money. They arent cheap and really unnecessary. Unless you go with a nicer amp and alot nicer subs i wouldnt even worry about it. Make sure you use 0 awg for your ground wire. And you should be good.

OH also, If your unsure about someone touching your car i wouldnt let them. Basically in the audio video world, If you touch someones car you bought it. Means if there are any problems in the car they just became yours. ANd 50$ is INSANELY cheap to hook a system up.

later....