We have many institutions running additional JavaScript without issue. You should be good to add any additional JavaScript to Canvas as long as you are following good programming practices. All of the Design Tools variables should be scoped to where they won't interfere with code you add. It does not matter if you add additional code above or below the Design Tools code. If there are errors in the JavaScript, it will break the tools wherever it occurs in that file. There are tons of things that you can do to break JavaScript but that would be true with or without Design Tools running at your instance.