Building a site with Twig PHP Template Engine

I've read through the documentation for Twig, but I don't quite understand how to connect the dots.

Let's say I create a file index.php which instantiates the Twig_Loader_Filesystem and Twig_Environment classes. I can load one template here using loadTemplate().

Individual page content is stored in .phtml or .html.twig files, which may link to other pages on the site. However, those would always link to another .php file, not the template.

What is the best way to abstract this process, so that I only need one php file for multiple templates? Htaccess? Some sort of router class? Are there any examples out there?