Well there are several things that can cause noise in a car stereo system. If the sound changes pitch with the engine then it is an accessory wire problem.
The best things to do that I would suggest would be to: 1)reground the amp, to the frame of the car if possible. Make sure that the ground is DIRECTLY touching bare metal and isn't near any power source. 2) Invest in shielded RCA cables. These can make a big difference in noise and sound quality, and again make sure they aren't near the power cable/accessory wire. 3) Check you're wiring size. Make sure that it's large enough for your amp *what size amp is it anyway and what size wiring are you using?* 4) Check all your wiring and try to keep it all separated. Sometimes just the acc. and the power wire being next to each other can cause distortion. 5) If all else fails then buy both a ground loop isolator and a noise reduction box. This should completely elliminate all noise from your stereo system.
