An answer I got from the REX staff over a problem I was having went like this ; " Windows 8  incorporates new folder security.

   To work properly both FSX and REX have to be installed outside any program file folders, otherwise it is really a lot of work to make it work properly."

    Right  now everything that is sim is in my external drive. The FSX is in it's own folder, the REX is in it's own folder. All add ons are the same way. Does the above statement suggest that I expand all my folders and leave them like that?

Everything is fine the way you have things now and the REX statement does not pertain to your file structure at this time.