You can either link the extra javascript into the layout.master file of your skin or in some cases you can embed it in the html view of the editor in the html content feature. Follow the instructions and examples of whatever plugin you are using except don't add the main jquery or jqueryui javascript since those are already included by mojoPortal.
If you can't get it working in the hmtl content feature you could implement a custom feature and add the extra javascript from server side code.
Hope that helps,
Joe