I have 1,3,8 and 10 to the right on my amp so the clip limiter is on and the low cut is off. If you have everything to the right you have it set up for bridged though, not single channel. Do you have the speaker wires running from the middle two terminals in bridged mode?
I have a balanced MiniDSP that boosts the signal to my amp and I set both gains at 8 o'clock for Audyssey. Then 11 o'clock is around 10dB hot and I clip around -10 to -15 on the receiver, though I often don't listen that loud. Clipping the amp is ~106dB at my couch during music for me.
You want to set the gain to 75dB during Audyssey because you want the end result to be between -3dB and +3dB. After that, you can bump up the sub level in the receiver or increase the gain on the amp. If you set it high to start with, then Audyssey will just have to make big cuts to get it back to reference level.
It's not a problem if the amp is clipping though. If you want it to clip at a higher volume on the receiver, just turn the gain down some. It would only be a problem, I think, if it wasn't output full power before it clips.
Living room: Definitive BP2000TL, CLR3000, BPVX, Quad SI 18" subs
Bedroom: Definitive BP30, CLR2000 Also have had: BP7000SC, BP8B, BP10B, BPX, Dayton 15" HF subs, Rythmik F15