This video might be helpful: Video: Embedding in Wordpress (Posts, Pages & Themes)
It looks like you have separated the Hype JavaScript file and are loading it within the footer of your page. It won't work if you separate the JS file from the Hype div.
Regarding issue with the height, I recommend placing your Hype div within another element with a height like this:
<div style="height:800px;">
<!-- place your Hype embed code here -->
</div>
That way you can be sure that there will be space in your theme for your document. You could also add this inline CSS to your Hype div: min-height:800px;
I'm Tumult!