I have essentially the same receiver, 2809ci. What amp will you use for the THT, and will there be anything connected between that amp and your receiver?
[EDIT: I remember you have the Dayton standalone amp. I would setup using Audyssey with the subsonic filter OFF, and then run distortion tests or play some real LFE material at the levels you will listen at, and if it sounds funny, switch the subsonic filter on. Then play with the parametric EQ to get the most distortion free sound.]
Audyssey does a damned good job of setting up EQ for you. You should just have to adjust the crossover settings (if that). Use all 8 positions when you do the setup, like it says in the Audyssey setup guide (also here on the AVS forum).