The best tip is to do it like you would in a ’normal’ site. Depending on what you want to achieve you could either simply add the JS to the template, or add it dynamically via a snippet (php code that will load the js according to some criteria), in a Template Variable (you can add a TV to the template and in the Manager define the content for that TV on each document) or a combination of methods.
If it is something that will be present throughout the site or is somehow tied to a specific section you could add it to the template and select that template for the pages that need the JS.
If it will be used only in specific instances yo can create a snippet to load it according to the defined criteria... for example load the JS if the document ID == xx or is a child of XX.
You can use a Checkbox TV (or a select TV) and have a snippet load a Chunk according to the TVs selected option (see the
wiki post on how to do this, remember to follow only the instructions for the Evolution version unless you are using Revolution).
Anyway, there are many options on how to do this depending on what you want to do and how you want to manage it. Hope this helps get you started and has not made you more confused.