Yamaha settings
Hydra,
I have a similar Yamaha receiver and it will do a manual grafic EQ of the center channel or an auto PEQ of all speakers. In my experience, the EQ feature on low end receivers is not that great and I leave the EQ off.
As sugested, you can manually adjust the speaker levels, distances, size, ect. instead of the auto setup MIC. I found the auto setup worked pretty well for speaker level and distance, but I manually adjusted all speakers to SMALL and the crossover setting with the sub.