For good result on your Audyssey calibration,
I suggest you first to return back to default setting on your receiver. Don't ask me why but that give better result if you are already did calibration. To make it, you have to press on VCR/DVD and power button together on your receiver. You must see CLEAR appear on your receiver.
Position your speakers the best cant, your could find a lot of reading about that, I suggest you Audyssey.com, all you need is there.
Important thing is to find a good position for your sub and it's pretty rare then we could set the sub in the optimal position, so place it in the middle of theroom, make it work, move yourself arround the room and where the bass sounds are higher, that must be the better spot. If that does'nt fit whit your feng shui, 1/3 lenght of the wall is almost a good position in many case.
Now your sub is positionning, set your receiver in direct mode and fine tune your main front left right speakers by listening music from CD player. No sub working, only stereo imaging. Toe in as required, adjust your bass by positionning your speaker farder or closer from the wall.
At this time your almost did the best of yourself for your sound. It's time to clean your room from any extra gadgets. Be sure then your room is exactly how it suppose to be. (no papers, cups box ... ready for decor mag shoothout).
Subwoofer: frenquency on max (you don't want double crossover) and gain in the middle way.
At this moment, shut off the refrigerator, all gismo that could sending signals, don't forget to close your cell. Be sure then your gonna have a fifteen minutes of really quiet room.
Plug your calibration mic, follow instruction and go.
After calibration done, save it, unplug the mic and only after that your could change the crossover on the setting. You can't change it before because Audyssey will not take it, moreover, maybe you chance it after the calibration, Audyssey will take it and adjust himself for different crossover.
If you want to set your HT as THX with 80Hz on every speakers, I still suggest you to maintain the sub crossover at 120Hz.
Finally, fine tune the sub by adjusting the gain to your taste and possibly changing the sub distance setting yourself to optimise. (Audyssey gonna adjust himself to new data).
In my case I got really, really good result by increasing farder the sub distance setting ( outside the reel position ) and by reducing the sub frequency. (120Hz on receiver and arround 120Hz on local (sub himself)).
As that, I listen movies with audyssey Eq. on and when I listen to music, audyssey Eq off in stereo mode, I just have to increase the sub decibel gain on the receiver and low frequency blend perfectly from the sub to my bookshelt speaker.
Good luck, give me feedback!