To get cahnches into mods you do this:
- create the mod, compile. This creates the .arz file
- get the .arz from the latest expnasion you have, put in place of the one from the mod + rename to mod
- compile again, return .arz to original location.
The game loads .arz file in this order: GD, AoM, FG. Files from GD, will be overriden by files in AoM, if a file with the same NAME and FOLDER PATH exists.
So to override files i suggest you use, the lates .arz you have, and have the folder path recreted exactly in your mod.
Another thing you can do is do it as a custom game and in here, for my mod i explain how to use main campaign chracters in a custom game.