Low tone noise's from amp.

Ok, i have a Sony CDX-MM8800 head unit and Street Wires Zero Noise 2.0 patch cords, running to a SoundStream Reference 705 amp. When im running the sub inputs from Sub Out on the head unit to Sub In on the amp, you can hear low end sounds. Like the head unit seeking to a certain track or the motorozed face opening. You can hear it through the subs. On the other hand when i run the sub inputs from channels 1-4 yuou dont hear the noise. I would like to keep in from the sub outs so i can conrtol the actual bass. What will it take to get those sounds out? I found some noise supressors on Crutchfield.com, will that do it? Let me know everyone. 

Run a temporary ground wire from the amp ground to the deck chassis and see if that fixes the problem.  If so, it would show a ground loop.  Wire the extra ground permanently if that is the case and solves the noise problem.  Otherwise, the sub out RCA may be picking up noise because it grounds to the deck chassis and either the RCA is not fitted tight or the deck has to be grounded better.  Try all these things.Build the box so that it performs well in the worst case scenario and, in return, it will reward you at all times.