The way you load any javascript has not really changed and is documented correctly in Adding Custom Javascript, previously you had to wait until the Pre-Render event to load scripts that depended on jQuery because if you registered them during page load event they would be registered before the main jQuery scripts and would come in above the main jquery scripts and therefore would not work, that is the only thing that has changed so now it doesn't matter much which event you register scripts in because the main jQuery scripts will always be first. But how you add scripts in mojoPortal is the same as in any ASP.NET application.
Hope that helps,
Joe