I have to second Alan's suggestion of getting the "Sound & Vision Home Theater Tune-Up" disc. I found this tune up disc suggested in a review and purchased it online. After going through the easy to understand steps, my HT sounded so much better. On top of that, being new to a lot of this and feeling somewhat in over my head, I came away with a lot of questions answered. It shows you how to use your SPL, how to calibrate your audio and video settings. The steps for calibrating the sub are easy to follow. On top of that it has some neat THX, DTS and Dolby Demo clips. I paid $16.55 for my disc online and found most to be around that price.

Auto calibration features on the Yamaha are pretty kewl, but there is no substitute for learning to do it yourself I think.

As for all the endless features, just keep playin with it for a week or so and youll figure out what mode sounds best with what to you.