Similar to Bretwalda's method, I just create custom subfolders (named for specific mods) under my Total War folder, copy the files and subfolders from my original Medieval folder (deleting the files inside SaveGames & TGAs), then apply the mods. Then highlight the Medieval_TW.EXE file in each mod folder, create and rename a shortcut for each one, and paste to the desktop.

You can see a picture here to use as an example:
https://img86.imageshack.us/my.php?i...folders2tq.jpg

Good Luck!