I don't change the original scripts at all... If I want to try something with them, I create a new script, copy all the code from the original, and edit the base object so that it uses the new script instead of the old.
This doesn't always work, though, especially for Activators that have their scripts baked the instant they are first loaded (and being persistent, that means the first time you load a game with them present). You can remove the old script from the Activator, but for all intents and purposes, it's still there in the game. I ran into this with one of my own mods (removed script in CK, tested in game, and it was still active), and counteracted by doing a bait-and-switch, which I really shouldn't have had to do in the first place because Papyrus's storage method is so utterly horribly designed. And the only reason I can see for it is complexity for the sake of complexity.