Tiki uses the Smarty template engine, and generally at least one PHP file and one Smarty template (.tpl) file, and sometimes several, are used to display a Tiki page, depending on the feature, section and so on.
The main template file that functions as a kind of skeleton for everything else is tiki.tpl. This file loads other template files for the various parts of the page - including header.tpl for the HTML head section, tiki-site_header.tpl for the site-specific items at the top of the page, and so on, and containing code to display the left and right side columns, the footer, and the main content at the center of the page.
More info: http://www.smarty.net/
Please see Template Tricks for more information about customizing templates.