Then you’ll need to change the section that calls what map to play for what planet from the standard maps to your custom map scripts. Change the name of that file to your custom GC name (again, basically just follow the patch instructions).
Then you’ll want to replace the init file from there with the CW init file from the modtools source files. If you’re just looking to take the standard GC and have your custom factions, firstly you need to understand how Shells work for making GCs, a quick look over the v1.3 patch notes should cover you for that, and get the basic custom GC files from in there too. Hi, so you wouldn’t be able to use this mod with different factions, however what you want to do sounds fairly straight forward.