First thing to do is check your gain on the amp. If it's turned too far up, this will cause feedback and you'll get whine in the output. If you turn the gain down and the whine stops, but the amp isn't loud enough anymore, you need a larger amplifier. gain is meant to balance the input stage of the amp with the line voltage from the head unit, so it should never be turned up farther than needed to get a clean signal.
If that's set properly and not the cause of the problem, then yes make sure the ground point is screwed down securely, and to bare, paintless metal chassis. Also make sure your signal (RCA) and power wires are not run close to any wiring for your ignition system for the engine, or near any crossover modules for component speakers. Both of these can induce EMI/RFI issues. Having power and signal wires next to each other, contrary to popular belief, will not cause a problem.
If the noise still persists, check the ground point for your head unit, too. Don't use the factory OE wiring harness for a ground wire, and run your own ground wire for the head unit, keeping the wire as short as feasibly possible, and ground to a good metal chassis ground point, free of paint and dirt etc.
If the problem STILL exists, it may be the RCA pre-outs of your head unit. Especially if it's a Pioneer. This problem can be addressed if this is the case. Otherwise, start at the top of my list and work down.
Thanks for the comments, I will work on that, thing sure is a pain. I didn't have this problem until I put a HO alternator on, but with 3 amps I almost needed it. The gain is down on the amp, it runs my mid-bass, but will check it all out. Thanks again.
maybe pinned RCA cable. try using a different RCA cable, and don't route it the same way as the original one. just leave it laying over the seats and such as a test cable.
also try using a different source, even if it's an mp3 player, CD player, whatever.. and see if the amp still makes noise.
sorry, "pinned" is an old CB radio term. a pinned cable is one that's been compromised. It happens with an RCA cable if it gets bent too sharply, or gets pinned under something sharp.
Yes try grounding the RCA shields. That was going to be my suggestion if you tried a different source and the noise went away at the amplifier. I have an mp3 player with a photo-to-RCA pair cable, so I can test amps with a separate source signal. It's a quick way to check at various points to find the problem.