Just saw this 18 minute video by John Dahl from THX discussing room modes (or peaks) and various ways to deal with them, including the use of multiple subwoofers, room treatments, and certain isolation and bass-trapping products. Its one of the better presentations on this topic.
As it says in the executive summary:
"This video gives a great overview of what it takes to tame the frequencies in your room below 200Hz - where the room really makes itself known. Taming bass response in a room is important as it can really make or break a sound system.
Additionally, with proper calculations, you can model how a room will interact with bass frequencies and better position your seating positions to . Among suggestions, John offers 5 tips to getting better control over your bass.
Choose a room with dimensions that are 5% different from each other
Don't position any seats in areas which have peaks or dips
Place subwoofers in such a way as to better diffract energy in the room
Use mechanical bass treatments (must be an active or resonant device in order to work)
The LAST thing you can do is equalize the room
This is a video every bass-head should watch and learn from. Everyone can do at least some of these steps in order to get better bass response and smooth out the bass so that you achieve better sound and a much more pleasing home theater experience."
Anyway I highly recommend everyone watch this well done educational video.
http://www.audioholics.com/news/trade-show-coverage/videos/thx-managing-bass-modes 
