I can't answer your questions Rat, but I can tell you I don't use the EQ part of my Setup on my Denon. I found it to make my speakers sound worse. Alan, from Axiom has said numerous times to turn that part off. It is ok to use the Auto Setup part that sets delay(distance), dB levels, and checks polarity. I think a few others have stated they turn off the Room EQ part, which should be seperate on the Onkyo as well.
At some point I plan to use Real Traps or other cd to chart out my room response and check for holes, then I can manually adjust those frequencies you mention to get a flat graph.
