At present (after July 2014 Steam update) the tool is obsolete - use this method instead to start your mod in steam.
Spoiler for original article:
Simply go into your Medieval II Total War folder and make a copy of medieval2.exe - then rename the copy to kingdoms.exe
You should now be able to start any mod with it's desktop shortcut - provided it is a kingdoms mod. Old mods based on the medieval2.exe require extensive modification before you will be able to play them in Steam.