>>I have a Yamaha 5790 with the YPOW(I know that's not right) but will that do a good job of calibrating it
Occasionally yes, normally no. Automatic calibration can do a good job of making your $3000 system sound like a $400 HT but with more "boom" in the bass
At minimum, learn how to use the test tones and manual level adjustments in your receiver. That probably won't help with the sub but with a bit of trial and error you can set the sub right by listening to a few different music tracks.
Even better, find someone who lives nearby with an SPL meter and an Avia disk and offer them beer & snacks
EDIT -- oh yeah... you might not pee your pants but the difference in sound is going to be incredible. If it isn't, you need to move the speakers around in the room some. The subwoofer in particular will probably take some experimentation to find the right spot. Do you know what a "sub crawl" is ?
Your new system is... well, just start lining up the CDs and DVDs and don't plan to sleep much the first night after you get it set up right.