I dont want the scripting I do in my plugin to show up in the master file, therefore showing up in other mods.

Does this mean I'll have to delete everything and download it again when I want to start a new mod?

Or have I missed something?

Not sure what you mean - scripts get embedded in saved games, so after removing several mods and putting in new ones it is best to start a new game.

But they do not modify Skyrim.esm or Update.esm and any changes you make in the CK only get saved in your esp. You cannot modify the master files.

~.~