You're placing your speakers in the optimal position for your listening. That doesn't mean that is the optimal position for the subs. Sub placement will be trial and error until you find the optimal placement.
Speakers on top of subwoofer
Is mounting a speaker on top of a sub a bad idea? Specifically, a Harbeth 40.x mounted with isolators on each corner so the cabinet can flex/breath on top of a Rythmyk E15 I have a limited amount of floor space and the Rythmyk is a little taller than a Tonteger which is a good thing since the Tons are a little short to place the tweeter around my ear height.