Nothing complicated like that sir.
Just install CFS3 wherever it wants to go and the same for WOFF.
They won't interfere with each other. Install CFS3 first as WOFF will look for it when it installs but in a entirely different area.
You have to do nothing special and you will have both in their own separate directories. Each will be all on its own and you can mod away on one and does nothing to the other.
Once WOFF has installed CFS3 and WOFF, and their folders and directories, have nothing to do with each other. Like two totally separate programs.