I have the same setup. After running the Audyssey calibration go in to the Onkyo speaker settings and change the crossover to 80hz for each speaker. Also, under Equalizer settings set to Audyssey. On the sub ( I have the SVS PC-12Plus) I have the gain set at the 10 o'clock position, do this before running the calibration!. Make sure you saved the calibration settings that Audyssey came up with then use that screen to adjust your sub levels (if needed).
Finally on the Audio Adjust screen under Audyssey turn off the Dynamic Volume. You can always turn it back on if the sound levels are all over the place.