If you search ‘fixed header’ or ‘fixed footer’ you’ll find a few different ways to do this. Here’s one method: Creating a Fixed Header Image
I personally would create the footer and header outside of Hype using standard CSS / HTML. It’s pretty quick with just a few lines of code. Here’s an example: http://jsfiddle.net/themorgantown/VKXZA/154/
If you set a high Z-index value in CSS for your header and footer, it will appear above your Hype document (use a value like 99).