First off, check out the FAQ, it ansewers all these questions and more. (specificaly the section on ground loops)

It's important that your ground is just as big as your positive wire. (Electrons are actualy flowing from negative to postive, or something?) Make sure you're running a big ground to the actual frame of the car - The seatbelt bolt or a screw into the bottom of the trunk seem to be favorites.

Then make sure to set your gains properly and not just turn them all the way up. The faq has a section on this too, I suspect.

Matthew