Shoutbox

No, that is not correct...

The scripts are global, i.e. when you disable it in on one account, the other ones gets disabled too...

The only way is to let the script check if the current user is the user for which it should run

So you have to add in the script something like:
function Name() {
   if (Messenger.MyEmail == "email@server.com") {
      //Normal function...
   }
}
in every function...
Also make sure when the function runs, it is logged in, or else Messenger.MyEmail will fail, to check if someone is logged in use if (Messenger.MyStatus > 0) { etc... }