This $('#your-flipper-id') simply represents the element to which you want to apply the flipper plugin. In this case it's searching for an element with the ID your-flipper-id. You can change that to be whatever you want.
I would suggest you put that code in a JS file that is called at the end of your HTML body.
You should have something like this:
<!DOCTYPE html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<title></title>
<link rel="stylesheet" href="css/style.css">
</head>
<body>
<!-- YOUR HTML HERE -->
<script type="application/javascript" src="js/jquery.min.js"></script>
<script type="application/javascript" src="js/flipper.min.js"></script>
<script type="application/javascript" src="js/main.js"></script>
</body>
</html>
In this case you load jQuery first, then your plugin and then your own javascript. Inside your own javascript file you would place that code. It should look something like this:
$(function() {
$('#your-flipper-id').flipper({
"width" : 500,<span class="Apple-tab-span" style="white-space:pre"> </span>// The total width of the widget.
"height" : 250,<span class="Apple-tab-span" style="white-space:pre"> </span>// The total height of the widget.
});
});
This will execute your code when the page is ready.