First of all, isn't Vi installed into the main folder of MTW? Why have them seperate? Or do you mean one MTW and one MTW/VI install?

Installing VI a second time from CD is not possible, because the installer detects your already installed version and is done with it.

Anyway, to have a second or third or whatever version of MTW/VI is pretty simple. You just copy the whole folder "Medieval - Total War" and insert/paste it at the same place (or some other), resulting in a new folder named "Copy of Medieval - Total War". You can run the exe from that folder (or create a shortcut to it on desktop). You can also rename the newly created folder into whatever mod is installed there, for example "Samurai Warlords"

You can also create the new folder first and then copy all that is in "Medieval - Total War" to this new folder.
Remember to install the mod into this new folder.

R'as