First thing to check is your grounding for the amp. Try another grounding point. It's best to use a point on the pan of the car with the paint sanded off; a bolt, nut and star washer for maximum contact with the body of the car.
One other thing is to properly adjust the gains on your amp. The gains will amplify the whole signal. If there is low level noise, it gets amplified too. Having the gains set too high will make noise really noticable that was always in the signal at an undetectable level.
I have two amps with my factory head unit (one for sub, a 4 channel for the speakers). I found that I got the best sound quality with the amp gains set very low. Unfortunately, this also gave me less volume than I wanted from the amps.
I ended up using a high quality adjustable line output converter to convert the speaker level outputs from the head unit to a signal that could be handled by the RCA inputs on my amp. This tended to boost the head unit's signal without increasing the noise.
I don't know whether I just used a connector that just had better shielding than the speaker level inputs in the amp, but it gave me the combination of quality sound volume I was looking for. The device I used was the Navone Engineering N-774V adjustable Hi-Q 4 Channel Adaptor. It is sold on the net via Dave Navone at:
http://www.davidnavone.com/index.htm
I think this item is their special this month.