Yeah it’s not all trivial.
Discourse is an EmberJS app.
Ideally JavaScript extensions should be written in the EmberJS framework using a Theme Component (or Plugin), the Discourse JavaScript API where appropriate and plugin outlets.
The main issue you will encounter in using ad hoc external scripts is making them fire at the right time.
To ensure that you need to link them to actions in a Component (which can be made to fire on insert or update)