I finally took the time to calibrate the 600's and the Onkyo 605 receiver. All I can say is wow! It does make a difference and there is some tweaking required (at least in my case). I used the Avia DVD and a Radioshack SPL meter.
In my case the calibration with the tones generated by the receiver was different than using the DVD. I settled on the DVD calibration as that's my main source and it truly calibrates the entire system, end to end, rather than just the receiver (via the receiver generated tones).
For what it's worth, I settled on 120Hz crossover, hookup via the receiver (not via the sub), LPF of LFE channel also set to 120Hz in the receiver.
The ProCinema package is great, I'm impressed both with the music and movies, but I'm just an average consumer. In the end, I'm glad I got the 600's, they sounded so good even in store where I'm sure they were not even calibrated.
FWIW, I settled on hooking the speakers up to the receiver directly, crossover at 120Hz, LPF of LFE channel also at 120Hz. I let Audyssey 2EQ do the initial calibration and left the distance and equalizer settings at what Audyssey determined and then just tweaked the individual speaker volumes with the DVD.