If you want to override a theme function not included in the basic list (block, box, comment, node, page), you need to tell PHPTemplate about it.
To do this, you need to create a template.php file in your theme's directory. This file must start with a PHP opening tag but the close tag is not needed and it is recommended that you omit it. Also included in the file are stubs for the theme overrides. These stubs instruct the engine what template file to use and which variables to pass to it.