It is better to create a third mod folder that is called something like "TDM + FQM", and leave the TDM and FQM mod folders alone (mostly for PBW compatibility and all).
The Maps and Savegames folders are definitely necessary for FQM Deluxe. Maps created in FQM Deluxe do not work in any other mods or the normal game. Maps created in any other mods or the normal game do not work in FQM Deluxe. So, the Maps folder is quite useful for preventing headaches later on. Also, the Savegame folder ensures that all of your savegames stay in the appropriates mods folders. This is especially useful when using the Mod Launcher.
