As for setting both of them up and deciding which you like the best, that's a good plan. Then again, whichever sounds the best, the gf is probably going to win.
I've never used YPAO, but I've used the equivalent system on my Pioneers. It not only sets speaker distances, it sets their levels, and (most importantly to me) adjusts equalizer settings to help compensate for your room acoustics and speaker characteristics.
The receiver has various listening modes that you can try to see if any of them sound good to you. It's entirely possible that you just don't like the Polks - I didn't really like the ones that I auditioned, but that's been over ten years ago.
A lot of people like Bose gear. Those cube systems have definite acoustic limitations, but if those limitations aren't apparent to you or don't bother you, then set it up and enjoy! I think it's good to come to forums to get info on how to get systems up and running well, and to learn about the pros/cons of different ones. In the end, though, enjoying what you get is the biggest thing.
