I called support and they answered my question. (Thanks Chase and Jeremy)
The custom events use jscript only, you don't need to specify any script tags, just enter your code directly.
In order to interact with other controls on the page you will need to go to that control and specify a control ID on the functionality tab.
If you want to define functions to be called throughout the page you can edit your web form and go to the behavior tab, all the way to the bottom you will see a script box, this is where you would enter your functions.
Hope this helps others.