Set it up manually and see how it sounds.
Set the crossover in the AVR to 120hz. Run the test tone generator feature and adjust by ear if you have to or get a SPL app for iOS or Android. It's better than nothing.
After adjusting the speakers somewhat, set the sub output on the AVR to maybe -2db and play something bass heavy and adjust the gain on the sub to what seems right without overdriving it. You should be able to hear when it's too much.
Then watch a movie or listen to some music for a while and see how it sounds. If you don't like it or there's no improvement then run YPAO again or a few more times to see what you get.
Klipsch RF-62II, RC-500, RS-400, SVS PC12+,
Def Tech SC8000
Harman Kardon AVR 1600
PS3, Apple TV, Sharp 70" Qattron