I had two installs in two different locations on my hard drive, one for SamWars, and one for MTW.VI. If I remember correctly, with older versions of SamWars you could play either from one install, but in the more recent ones, certain elements of the original MTW install are disabled by the mod (can't remember which ones). R'as or one of the other SamWars gurus can clarify specifically.

I prefer VI over vanilla MTW; like Warlord Edition, VI adds a lot of color and variety to the original game, including new campaign scenarios, and fixes a few things.