%%ELEMENT_ID%% will be replaced with the actual ID of the element.
As is default with WordPress, jQuery is loaded automatically. To use jQuery, write jQuery('...'), not $('...').
- create a plugin to enqueue them with wp_enqueue_script
- upload them somewhere and insert the necessary <script> tags
If you have code that looks like <script src='somescript.js /> from your typography, analytics, or other 3rd party cloud provider, read this article on adding code to <head> or before </body>.