Subwoofer placement shouldn't be purely aesthetic. If you want the best bass in your room, you'd have to do some work for it. Read the Crawl for bass article on the main site. -
https://www.audioholics.com/home-theater-connection/crawling-for-bass-subwoofer-placement.
In another note, I did not hear much positive feedback about the accuracy (or lack of it) for the AccuEQ system. You may be better off trusting your own ears and doing manual turning with a SPL meter or going with the free RoomEQ Wizard (REW) system, assuming you buy a calibrated measuring mic.
Lastly, since your main speakers are small, getting a 120Hz crossover shouldn't be surprising.