I'm looking forward to answers to this question too! I'm in the same boat. I do notice that Audyssey does set the distance to the sub, which turns out greater than the actual distance, and I've learned to keep the calculated distance, as the increase has something to do with the delay in the sub circuitry itself (don't quote me on that).
I generally am constantly tweaking the gain control knob on the sub depending what I'm listening to, for BR, or TV content, or regular DVD, it all seems to change the 'loudness' of the sub and I am always tweaking the gain to where I want it.
Again, I look foward to learning any more tweaks I can do in the Onkyo setup for the sub.