Hi Dylan,
The javascript your Lithium Community adds gets added near the bottom of the page so you need to make sure that your javascript runs below it if you'd like to use the jQuery libraries we add (so you don't have to add it again which will increase the loading time of the page). We have a special directive you can use in any component called <@liaAddScript> that allows you to add javascript that will be placed just below the javascript added by the Lithium community core app. This page has a good example of using the <@liaAddScript> directive:
http://community.lithium.com/t5/Developers-Discussion/Call-Endpoint-from-Custom-Component/m-p/159554#M6337
-Doug