When I am not using my woofer, I usually turn on a set of 6x9's I have in the back, to give people riding back there more sound, and I think it sounds better my self. Anyways, whenever they are on, there is always a real whiney noise in the background. I think it has to do with the car running, as when I slow down the sound is more noticeable, and at idle it sounds bad unless the volume is loud enough to drown it out.
I had the same problem with my system. I just installed a alternator suppresor/car noise filter to over come this problem. They cost around $30 but if u want to get rid of the problem, then this is what u will need. do some research on the internet and it some sites explain what to do, why the noise is there and how to overcome it.