From what I've read on this forum, the Audyssey system tends to set all speakers to "Large" (my Pioneer does the same thing, even though it has a different auto set-up system). This is generally not what you'll want.
First, you'll want to set the satellite speakers to "small." As for the cross-over, people tend to recommend 80 Hz as the right place to start because that's the THX standard setting. You can play around with it and see what sounds good to you, but that's generally a good setting.
EDIT: Once again, avaserfi beat me to it. So fast...so fast.
