[lkchris]

The OE radio is set up for the equivalent of front speakers only.

Your aftermarket radio provides for front and rear speakers, but you don't have rear speakers.

The AMP that you have does that but also provides a split to the door speakers, which are subwoofers and NOT rear speakers.

Without adding rear speakers, your best bet imho is to run the front outputs from your new radio to your original amp, just as was the case with your original radio.