If the mod uses it's own folder in the GameData folder, you just treat that folder as another base folder. For example, pk3s loaded from /GameData/base will be loaded when you launch the mod (EY4) AND also load any pk3 you put in the EY4 folder. If you want to replace things in the mod, you can make a pk3 to do so, but you must put it in the EY4 folder for it to overwrite, and also make sure the file name of the new pk3 comes after the pk3s alphabetically (so just put z at the beginning of the name). Don't put the new pk3 in the base folder. It needs to go in the mod's folder. Especially if you're actually replacing the original PK3. Same place you took it from.