If I may....
Find something to set one of the speakers on (one speaker) like a box or something to get it up off of the floor and away from any walls.
Get 1 meter away with the mic, on tweeter level, and then shoot a response.
Then the most important part: Gate the time window to limit only about a 4ms time window. The first arrival will take about 2.75ms to arrive, so start it just before that (about 2.7ms), then cut it off at 6.7ms.
Also set your range to go from 200Hz and up. At one meter you are not far enough away to accurately measure below that anyway.
An in room response measurement, like you are taking, will only tell you two things. It will tell you if the subs are in phase with your main speakers, and it will tell you what the room effects are and where.
Please note though that you can not look at a room response of both speakers playing together, at the same time, with the same signal. If you run them both together, at the same time, then one will just cancel out the other in some places, while causing peaks in other places. And then you'll get a mess much like what you have posted.