I always enjoy stopping by here and checking out the exploits of this sub
What you're experiencing really isn't that unusual. I would recommend one sub up near the front, with the driver either facing the wall, or sideways so the driver acoustic output is near the front wall boundary. I'd place that sub approximately 1/4 to 1/3 of the width. Now I'd place the second sub similarly, however in the rear of the HT, and opposite diagonally if possible.
Your subs, arrayed in this manner, should significantly smooth modally induced peaks and nulls in the room. By spreading LF sources on each side of a hypothetical mid-point of the room, room modes in that direction are addressed. In your case, your subs spread across both the front to back axis, as well as the left to right axis, this should yield significant response smoothing at the LP. Now certainly every room is different, and boundary (walls, floor, ceiling etc.)impedances can prevent optimal results from the method I suggested, but it should offer some solid results and perhaps a platform from which you can continue further experiments.
If you don't have any measuring gear/software, this is much more difficult. Something like OmniMic from Parts-Express would simplify your optimization tasks immensely. It's very easy to use and you can be up and measuring in minutes. However, with the Galaxy meter, you need a freq chart and plot some points and make some graphs. I believe those charts are in various places on-line. Rives used to have one,...maybe Thomas at The Cult has one.
Best of luck