Have you got to the part where it says if your system isn't minimum phase then parametric EQ isn't going to fix it?

From this I take it that the first step should be identifying and fixing any glaring problems in your room. Then re-run REW and tune in the parametric EQ.

From that standpoint I would think REW can be run with your current setup to identify the room problems and, incidentally, get some experience with REW.