did you buy aftermarket harnesses? or did you try and wire it in yourself? I bought an install kit that came with two wiring harnesses that plugged right into my factory wiring and everything worked fine..
the black box under the seat is an amp for the factory stereo.. Ive taken mine out since I put an aftermarket HU in and had no problems..
Check out
http://www.cygnusx1.net/supra/librar.../in/IN_01.html
and go to the wiring section and then go to the radio.. Might help you out, what year is your car?