Capacity is a versatile framework which helps you to construct your page by focusing on the content. Your pages will be simple PHP-files which include predefined header and footer. This header/footer layout the page, you only provide the real content and menu structure.
Any normal page just contains:
<?php $page_title = "Page Title"; include "header.inc"; ?>; Content of the web page <?php include "footer.inc"; ?>
For each subsite, a site.inc in the toplevel directory of this page, which would be equal to the later documentroot on the server in many cases, may be created. This include is used by the header.inc, it should contain some information about your site, like it's name and the email address of the webmaster, this will be used by header/footer to setup the page correct.