Rat Shak eter is set to "C" weighting and slow response then get your first main to read 75 or 80db, once you get that set you simply match all speakers to that number....its very simple and take less then 3 minues. For the sub your phase in mainly in relation to placement in room, if sub is very close to mains or in front of room "0" is fine.if its in middle or rear you would play with phase up to "180" to blend its output with mains.
One simple test could be done if you have a DVD movie that is "THX" as there is a useful phase test for all speakers to make sure you hooed up speakers making sure positive didnt get mixed up with negative on either end, when a speaker is out of phase it will sound very disperse and hard to place exactly where the sound is coming from.
There are no real settings that are useful other than personal prefrence on your Onkyo as long as you have speakers set correctly for size, crossover and disance from your seat and have digital inputs set up correct that is all that is critical to start learning what you prefer.
If you want any help let me know and I can walk you hru all of this on phone, we can get youup and runing in short order............cheers