Heh, the other day I re-installed Rome to try some more mods.
Did all that, copied it, installed EB on the copy, and then uninstalled the vanilla. I could still play EB, but when I put the disc in I had the option of re-installing Rome!

(I have, everything works great)

Btw, patch Rome before you copy it, to be sure. I think that's what kept several mods working on my pc (despite the fact that when I checked the games' version, they all said the correct one..)