Nazar, thanks for responding. I am hopeful that this system sounds better than what I'm getting out of it right now and hope to get this figured out. I'm using both RCA outputs on the deck as shown in here (except going to 1 amp instead of 2) front set is going to Ch1&Ch2 on the amp input, sub is going to sub on the amp:
Also it seems that the deck can be changed to select subwoofer output but all this appears to do is enable the lpf on the deck itself and changes the fader options since there are no rear speakers.
I will try again turning on the subwoofer output and setting the lpf to 80hz to match the amp LPF. Or just turn off the lpf on the amp and let the deck do it. I would think that leaving the deck output set to full would be the way to go since the amp is handling the lpf in my current configuration.