You can start using Audyssey sir. May microphone kasama yang Onkyo to calibrate time alignment into your listening position(s). Yun lang Audyssey may sound thin sa bass, so after the calibration, you can just adjust the bass/sub gain on the AVR manually up to your liking.
On the speaker setup, set the front speaker to large if it is a floor stander. For listening modes, I just let the AVR choose whatever is best depending on the source. Because sometimes, when we do Direct Mode, which supposedly bypasses the internal DAC of the AVR, masyadong mahina ang kinakalabasan. So I leave the processing of the AVR by itself.