Have you checked out the Cult of the Infinitely Baffled yet? Lots of good info there.
I just installed two of the IB318's in my wall, on a 1 1/4" MDF panel. I added four 2x4s between the wall studs and the roof rafters to keep the wall from vibrating too much. After that, I had very few room rattles to deal with. And don't buy the MDF at Lowe's or Home Depot. It's not very dense. I looked around at some local lumber/veneer suppliers, and found "industrial" MDF. Same price, same machining qualities, but a much denser, heavier substrate.
The other option is a manifold (box). This takes more time to manufacture, but it won't stress your ceiling structure as much, as the vibrations from the speakers are self-cancelling (assuming you mount them on opposite walls of the manifold.) I'm pretty sure the IB318's can be mounted horizontally, but I would check with FI first.
As to which option sounds the best, I can't really say. I know my setup, in a 2300 cu. ft. room, is amazing. If your room is larger, you could add two more IB318's to the manifold without too much trouble. I left myself the option of installing two more IB318's on the opposite wall, but after running REW, I'm flat down to 5 Hz, with plenty of SPL. Another nice thing about IB subs in general is that they don't require much power to drive them. I'm using a Monolith 7x200W amp, which isn't being taxed, as the output from the MiniDSP is less than the input sensitivity of the amp. So even if I turned the Master Volume all the way up, the amp won't get enough input voltage to run at 200 watts. (350 watts, actually, as I bought the 4 ohm version of the IB318.) I'm running each driver with its own channel of amplification.
Hope this helps. I think you'd be happy with the Sound Quality going either way.