Oh, I thought the mic was usually included with AVRs rather than optional.
Keep the treble/bass controls at zero/neutral rather than turning up the bass. You want the sub to do the work, not DSP.
The manual details the crossover setup:
https://www.intl.onkyo.com/downloads/manuals/pdf/tx-nr646_bas_adv_manual_en.pdf
I think it should be in the "speaker" menu, and is then adjusted on a per-speaker basis.
If the issue is that the sub doesn't get loud enough and bottoms-out when you turn it up, even when the crossover is set at or below 100Hz, it may just be that it's under-sized or poorly placed?
I'm not seeing a lot of information for that model but it looks like an 8" sub.
Check that all of your speakers and the subwoofer are properly in phase too. Flicking the phase switch to 180° would be the quickest way to check if it's in phase or not (being out of phase will cancel out the low frequencies).