Help to understand web site structure using PHP

Hello and good Year for all, I'm new to web developpment and PHP. I'm learning about *.inc,*.php, index.php, require(....), include(....), index.html....., Please can you telling me where I can find a detailled Doc on how to manage web site using PHP? More particularly, I want to know what is the structure of site that PHP (*.inc, *.php....) uses generaly, where I can have a clear design which can understanding me the directoy structure or arboscence to setup web site using PHP? What files to put here or not? What structure of files (like Linux directory) you can suggest to build a site web? Thanks