The beauty of the script is that the home page is not a script, but a normal HTML page.
Therefore, there is no need for a header and footer for the home page.
You can simply load the index.html file into any HTML editor such as Dreamweaver or Frontpage and edit your homepage just the way you like without the fear of messing up with PHP files.
Also, Blog, FAQ, Contact Us, etc, are just normal HTML pages, and these can be created using your HTML editor.
(If you do not see a homepage, please rename example.html to index.html)
For advanced customization, there is a header.php and footer.php in the users/ directory.