As far as the surrounds go, its only a matter of having the proper distance set from the center seat position to each one.
As for the subs, with two, each does not need to have as high a db output compared to only using one. Try the subs with one next to the door on the 12' wall, on the side of the seats. Place the other sub between the left main and opening to the hallway. That will get rid of the boom.
Also, have you tried both subs up front to either sides of the tv?