Well whatever works the best for you is the way to go. There really is no "best" way. Everyone has a unique grow area/situation.

You could install hooks in the ceiling of your box to hang the CFLs from, or like you said, you could have two boxes. That way, if timed right, you could have two grows going simultaneously!

Also, you're probably better off going with the 400w, that way you are prepared for any future grows.