If I edit an existing quest script, should I overwrite it or make a new one and have the quest use that editing script. Let's say that I do overwrite that and disable a mod that uses the editing script. Will the game use the original or the edited script?

Your game save can become whats called 'dirty', or in the worse case, 'corrupt'.

The state of the script, if it has been activated, will be saved in your save game. Changing that script could cause some corruption. Making a new script could solve some of the problems.