Hi brad,
Audyssey can be a bit confusing at first. I'm adding a link to the FAQ section at Audyssey which should help ansewer your questions.
With your speakers I would set the speaker size to small and use an 80hz or 60hz crossover with the mains and 8ohz with everything else. If the receiver doesn't offer individual crossovers for each channel then go with 80hz. Make sure the crossover is disabled on the sub or turned all the way up. Set the phase to 0 to start with and adjust if needed.
When taking measurements make sure the mic is on a small tri-pod for best results.
Let me know if you have any firther questions.
http://www.audyssey.com/technology/faq.html