Yamaha PEQ vs GEQ equalizer settings and sub settings

[Canuck31]

So I just re-calibrated my 5.2 setup with my Yamaha RX-V481 receiver. First of all YPAO put measurements are all over the place (such as distance and levels) so I had to re-adjust those. It set my crossover at 100Hz instead of 80Hz and always sets my front L/R to "large". I also always get a "W:3 Level Error" and the subwoofer indicator on the display flashes. Plus it set my sub level to the lowest possible level of -10. The volume level on the rear of the subs is half (I'm using dual subs with a Y-splitter). In any event after tweaking the settings the surround overall sounds great and dialog is easy to understand. But the sub levels I think need to be tweaked. But I notice when going into the equalizer settings that when on PEQ (which is the results of YPAO) it sound more surround-like even for just stereo music whereas the GEQ or OFF settings (both sound the same) are more flat. It doesn't sound bad just not as full. Has anyone here turned off the EQ on their Yamaha receiver or played with the GEQ settings? I noticed you can tweak it for each speaker and not just an overall adjustment. That seems like it would take a lot of time but has anyone done that? Also should I keep the volume knob on the rear of the subs at half and simply adjust the level in the receiver settings?