My sugestion is to produce alternate eep_scenarios that allow to "install" it without change the original files. Most of changes eep packcage introduces do not need changes, since you can alter the scenario file to read files with others names (for sample, instead of change the monarchs file, use one with other name; instead of use the alternate ai files, use another in the country file. I do this with good results, all files in eep must be defined in inc files, so there are no need to upgrades, just to be another option.