How did you get a stock amp to work with an aftermarket HU?
I had to rewire that aftermarket harness that was sold to me, the one with the elongated L connect with the pins for the power, and the 8 pin black box square connector.
I went through a number of cd players blowing RCA outputs for hooking up to my amplifier until I finally stumbled across something stupid, yet great at the same time. I dont know if this will work for any one else but if you hook this aftermarket 'harness' up that they sell and it sounds like absolute crap, the reason is the wiring for the harness (cd player/deck) to the actual incorrect harness itsself (the converting wiring harness you connect to your black 8 pin box and your power connector which is elongated with the L connect pin on one side) well, I had major problems, went through about 2 - 3 head units until I finally figured out what the problem is.
The JBL onboard amplifier takes LOW LEVEL inputs from your factory amp and then BOOST them bigtime to produce the sound you hear with your stock radio, well since our aftermarket (my pioneer/blaupunkt/kenwood/sony) ect would put out a high level (say 40watts times 4 at 4 ohms) is a lot for those low level inputs.
I always kept wondering why my RCA outputs from my aftermarket cd players would go out (smoke would roll outside the cd player when I first hookedup the power and everything wiring harness wise was correct also... so) kept making me more

and eventually I rewired the entire thing.... I was wiring into the actual speaker outputs from the cd player itsself and taking the inputs from those speakers and tying capacitors to them to run to my amp for their low level singal with rca cables using 2 channels, which created a popping noise when changing tracks... back to square one.
So somehow I had it all apart in front of me and I touched one of the wires to the shielding of the rca cabling, and amazingly enough sound which was static popping sound came out of the speaker, I could then ID what speaker wire was going to what speaker, and I eventually was able to tie them all back to their location using this method. Now I would not recommend using this method because the RCA cable of mine already had been smoked and there was no output in the RCA to run to my amp anyways.
But, I am unsure if this would work for anyone else, if I can recall, the ignition was on but the cd player was not on when I did this and it would create a static noise in each speaker as I touched each wire to the rca output shielding (the ground / outside of the RCA's) which told me there was a common ground system going on, and I had found that the Front + - ended up being like Rear + and front - for example. The coloring and the actual labeling of the wiring scheme was totally incorrect for my harness I bought so BEWARE of this.
I know now that I have mine balanced and tuned and sounds absolutely awsome, I had shrinkwrapped all the soldiered connections within the dashboard for maximum life and no shorts.
So dumb luck for me I was able to figure out what wire went to which speaker (BLACK BOX) and I wired it correctly.
I am not going to rip my dash out and show everyone but that is how I was able to finally figure out what harness wire went to what
and Ignore the orange wires they are illuminations....
cd player is not going to brighten or dimm due to you raising your brigness knob on the left side of the steering wheel column...
Well thats a book hope you enjoy.