DevShed.com has the third part of the Building a Site Engine Using PHP series working on the foundation they've set before.

In this third article of the series, I'll show you how the database and directories should be set up. I'll also talk about the how to create, install, and use a content block, which mostly relies on arrays and array functions. I'll cover proper authentication methods for such a project so that multiple sites can run off the same users table in the database, while not barring a username from being used on a site because it is being use on another, all the while keeping the authentication accurate and secure from break-ins.

They use a system of plugins and templates in an organized directory structure to create the structure behind the display. They then create several tables in the database to hold the content, and a discussion about "the block system".