First off, jQuery and Social Engine don't always play nice. SocialEngine comes with Mootools, so using it will make your life a bit easier. That said, you can add reference to your JS files into: applicationmodulesCorelayoutsscriptsdefault.tpl
.
Then you will find that you have namespace conflicts between jQuery and Mootools. To resolve this you will need to change the namespace of all resulting jQuery by adding the following line at the head of the same file.
var $j = jQuery.noConflict();
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