You need to try and have your subs the same distance from the primary seat as possible. Mine are spaced out around the room about 12 ft from the main seat. If you follow the Audyssey setup guide written by a fellow AVS member, it talks about calibrating the subs prior to using Audyssey. They use 80dB, but I found that set my dB levels on my Denon to low. So I used 75dB.
If you have a Radio Shack SPL meter, just run the manual test tones in the Denon found under Speaker Setup. Turn only one of your subs on and calibrate it to 75dB's, phase set to 0, and turn the crossover knob on the subs to their highest setting, since the receiver will be doing the bass management. Then, turn the first sub off, and calibrate the second sub the same way. Then turn them both on, and your ready to calibrate with Audyssey.
Also, you don't want the seat backs of your couch or chairs to get in the way of the mic, they can cause reflections and skew the results. I reclined my seats back, and used a camera tripod to place the mic in the approx ear position for each measurement.
I have two rows of seating, so I ran the first measurement from the primary seat in the front row, 4-6 in the other seats, and the following 2 halfway between the two rows.
One trick I found in the setup guide is after the first measurement, go ahead and calculate and save the data. Then you can check to see where it set your dB levels for the sub channel. Then Denon has a -12 to +12dB swing for the levels, and you don't want to be at the extreem ends of this range, so you may have to adjust your volume(gain) on the subs and rerun until you get say + or - 3dB from the 0 position on the receiver.
After you are all done, for speakers set to Large, you want to change that to small. Also, for those channels set to large, you will have to bump up the crossover from 40hz to 60or80hz. Also the LFE crossover in the Denon (which is actually a low pass filter) this needs to be set to 120hz per Audyssey.
