In general, you want to place your JavaScript at the bottom of the page because it will normally reduce the display time of your page. You can find libraries imported in the header sometimes, but either way you need to declare your functions before you use them.
http://www.w3schools.com/js/js_whereto.asp
index.html
<!DOCTYPE html>
<html>
<head>
<!-- You could put this here and it would still work -->
<!-- But it is good practice to put it at the bottom -->
<!--<script src="hello.js"></script>-->
</head>
<body>
<p id="external">Hi</p>
<!-- This first -->
<script src="hello.js"></script>
<!-- Then you can call it -->
<script type="text/javascript">
externalFunction();
</script>
</body>
</html>
hello.js
function externalFunction() {
document.getElementById("external").innerHTML = "Hello World!!!";
}
Plunker here.
Hope this helps.