Delete the registry files and reinstall RTW in a different folder (if you want to keep RTR, which by "duel installation" I'm assuming you want to), then go copy/move your vanilla savegame.
Personally, I'd go for Uninstall everything save the savegames -> Fresh install -> Two copies of "Data" in the same folder (I name the other DataRTR or DataRTW, whichever's appropriate) -> Patches for both "Data"s and modding for the other -> Rename when necessary.