Sub gain (volume) should be set at about 50 percent to begin... when you run Audyssey, it will have you adjust it to about 73dB. Follow the instructions in audyssey, let it set the distance and levels in the AVR, and for most... you should be good to go. (Oh, and then TURN IT OFF... unless you like the way it sounds, of course.)
Low Pass Filter: bypass
Phase: 0
Parametric EQ, Polarity, and the room gain compensation: don't play with yet... you'll need to learn what those do and how they operate. In time you will!

But this should get you started!