I've never used jQuery but with regular JS you just put your script in the <head> section of your page. Like this..
<head>
<script type="text/javascript">
Your JS Code here
</script>
</head>
Or you can call it externally using <script type="text/javascript" src="yourcode.js"></script>
Then add that .js file to your root directory (or any other, just change the path).
Hope that helps.
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