IMHO, the best way to use the EMU is to copy your EQ directory to another (call it EMU) and just run eqw out of that directory instead of out of your "live" folder. This way you can have both with just 2 icons on your desktop without having to switch files (or even run both at the same time if you are so inclined).
This is how I do it and i never have problems with having to back things up
