Sheep said:
Put your subs where you sit, and crawl around the room until you find a spot that gives you that same bass you like. Then put the subwoofers there.
Good info there from Sheep.
What's basically happening is that you're getting room/speaker interaction problems. It happens, to different degrees, in every room.
If you were to walk around your room with a mic or SPL meter, monitoring different bass frequencies, you'd see peaks (boom) and nulls (no bass) all over the place. Oh, and different frequencies will have peaks and nulls in different places.
Try what Sheep has recommended. You could/should also try for a seating position that's 38% of the length of your room. I.e. if your room was 100ft long (I can dream anyway) then you'd want to sit 38ft from the front wall - this tends to have the best response for your room. The worst place to sit is usually halfway between two opposing walls (i.e in the middle).
If you want to spend some time reading up about this, then you could try F. Alton Everest's "Master Handbook of Acoustics", or for useful articles, and products to combat room acoustic issues, look at
http://www.realtraps.com.