You are getting standing waves if it's boomy, need to find what frequency is causing it, then change it.
Find a song that starts the boom, walk around the room to see if there are places where it doesn't boom. If it's a large part of the room, move your sub, so your listing position sounds good.
If it is in the whole room, adjust the PEQ, always go down if you can, trying not to boost anything, just cut.
If it's still an issue, do both, move the sub, and adjust PEQ. Might also need to adjust the XO point, as it could be interaction between the sub and mains.