All you put in your .js file is the javascript - nothing else. It should just be a bunch of functions and such. The css still stays in the template, along with the calls for the other javascript. The stuff that goes in your .js file will start right in here:
HTML Code:
<script type="text/javascript">
//<![CDATA[
// Global Variables
// set map variable
Take all the javascript you are posting in that tag and throw it into your .js file.