Hi: The crossover is in the sub. I have it set for 80 Hz, but I seem to have to change it for every different CD I put in. I'll back it down to 40 Hz as you have recommended. Volume on the sub is at 11 o'clock. In regards to the phase, I've tried switching between 0 degrees and 180 degrees - no discernable difference. I just can't seem to blend the sub with the M60's. But if I connect the amp to the sub's LFE input, I get the full spectrum of music - it just sounds like an ordinary speaker.
You are right in that I was listening to the sub, rather than the M60's and sub together - I'll correct that flaw in further testing.
I'm using a lot of organ music, the theme song to Jurrasic Park, and Time Warps. My son also has some music with a lot of bass - boy is that painful to listen to.