The method I prefer is to use a custom .BAT file that looks like this:
Code:
medieval2.exe --features.mod=RheddGovMod --features.editor
Replace "RheddGovMod" with the name of your mod, and it'll run your mod, but use the standard .CFG file. No need for duplicate .CFGs.

The "--features.editor" part isn't necessary, of course. It just enables the map editor.