If you would post your relevant code it would be easier ;-) but anyways, this is one possible way of doing it:
<html>
<head>
<script type="text/javascript" src="path_to_js/jquery.js"></script>
<script type="text/javascript" src="path_to_js/your_js_code.js"></script>
...
</head>...
and in the file your_js_code.js you'll have:
... /* All your modules and functions here */
/* DOM loading ready */
$(document).ready(function () {
call_your_methods_here();
});
By the way, it is usually better to load your JS files at the very end of the <body>
in the HTML, that way your HTML starts displaying first and the user "sees" your page faster, while the JS code is still loading.