Actaully all of the wiring is in the dash. I will run the RCA's out from the head unit (and to the amp/eq) out a different direction than the wiring harness and see if that makes a difference.
I will also add a ground strap to both the head unit and amp/eq.
Basically what I have is small in dash EQ with built in amp running off the RCA output from the head unit. Both are powered and grounded by using the stock stereo wiring harness (with an adapter that breaks out all of the wiring).