Here's my quick 'n' dirty "how to" Audyssey:

1. Set the gain control on your sub to roughly "noon", crank the LPF knob fully clockwise to disable the sub's LPF
(or use the "crossover disable" switch if your sub has one) and set the Phase to "0".

2. Run Audyssey at the first position (all speakers + sub(s)), calculate, store and then check the levels in your receiver's speaker set-up menu.
i) If the speaker levels are at around 0dB, and the sub level is within ~6dB of the level of the speakers, proceed to step 3.
ii) If the sub level is too low, lower the gain on the sub itself; if the sub level is too high, raise the gain on the sub itself; then re-run step 2.

3. Run Audyssey at all 6-8 positions, calculate and store. Then go into the speaker set-up menu and:
- set all speakers to "small";
- set the speaker crossovers to the levels suited to your speakers (for good-quality bookshelf speakers and larger, that's usually 80Hz);
- leave the LPF of LFE at 120Hz; and
- bump the level of the sub by ~3-6dB (if desired) but do NOT touch the gain control on the sub itself.