General architectural approach to Drupal for a project
This is a common grey area for new developers to Drupal. The root for every "page" is index.php. There is no "page" per se, every dynamically generated "page" is a container. Regions (found in either /themes/bartik/bartik.info file in Drupal 7 installations without any changes or additions to Drupal core yet) establish the sections of the container that you can add different types of content (i.e., blocks, menus, views, etal.) I would recommend reading about the bootstrap process for Drupal, it is during bootstrap that everything gets called on a url by url basis. Using the Drupal interface and adding modules adds ways to "generate" or "contain" different types of content. There are over 10,000 modules (and counting) to add functionality to the Drupal enviroment. There are, generally, a handful of recommended modules that provide the most cohesive and robust ways to develop almost anything within your Drupal site that are recommended.  This ultimate flexibility takes a little time to grasp and work with but once you do, you never want to go back.