A very basic mod manager which will detect the mod packs you have in your ETW\data directory and allow you to enable/disable and order them as you please. When you launch the game from the mod manager, your user.empire_script.txt will be updated according
Once you check which mods you want enabled, you have to run the game from Mod Manager at least once to set the script up. After that, you can run the game any way.
**Just ensure the Mod Manager remains on your Desktop**