The mixed elements are indeed hard to separate. Typically I group the six channel wavs so that an edit to one will make an edit to all, then temporarily break that grouping if I need to make a tweak to the center channel. Occasionally I've needed to flow in a bit of music from the soundtrack here and there, but mostly I've been able to mix the sound by crossfading the DVD's L&R channels while leaving a gap or a patch from another area in the C channel.

I can readily think of two examples where I had to find a snippet of music from the CD soundtrack:

Killing Jake Lloyd's "Yippieeeee" when he was freed, and shortening Vaders "Noooooooooooooo." I'm sure there are others but those two stick out in my mind.