What you are describing is a problem with room modes. Please look at here for description:
https://en.wikipedia.org/wiki/Room_modes
First of all you have to lower the volume of the subwoofer. The best one is that you recognize when it's turned off. The next step is the correct placement of the sub. Put it down somewhere in your room, let music play with deep bass and crawl across the floor. The place where the bass sounds best, is the optimum place for the subwoofer. You can also position bass traps in the room corners, but the best way to eliminate room modes is the usage of a room correction like ARC, Dirac or MiniDSP. There are many threads in the Forum about it.