You need to post your settings from the deck. The 80PRS has a lot of tweaking capabilities, which is also room for a lot of undesirable results. I just installed mine last week, and finally figured out where everything is. Go through and write down each of your settings. That, or completely reset the audio settings on the deck and start over. I believe there is a button behind the faceplate, but you can google it as well, it's in the manual.
The auto EQ/TA that you said you ran tends to set the bass levels way lower than people here generally like to set their bass. It blends seamlessly for SQ where it sets it usually, but around here we like it louder. You can set your subwoofer level under "subwoofer 2". Sometimes the sub will be as low as -24dB. You can turn that up and see if you get sub output. But only tweeter output and nothing lower, including the sub which is a totally seperate channel, is a little weird. Sounds like it might also be a crossover or even amp setting problem. Once you are sure you have the deck set right, then you will have to go back and set your gains again, more than likely.