Beginner Question

Hi, I have learned as lot about PHP but I still dont know how do they build PHP based web sites. I need to build a complete PHP site with a lot of content and integrate CSS,javaScript and a lot of other stuff (for the school) (Complete site for example. www.domain1.com/index.php or www.domain2.co/about?set=p1) I want to know how are the sites built, do they build for each page a PHP script or do they build just a couple of scripts and a database full of content and just retrieve and delete,edit,show database information? I know that when I see in the sites url php? that means that site has a database, right...? Either way I would be very gratefull if you could you give me a detailed explanation of the process of building a PHP/MySQL site (I know to write scripts in PHP so im not a total beginner). Thank you very much in advance!! P.S Please, I understand this could be a stupid question but please bare with me... :)