WebReference.com has the second part of their "Core Web Application Development with PHP and MySQL" series posted today that features a look into the flow of the application.

Every web application that you write will have a different layout, flow of execution, and way of behaving. It can prove helpful to follow some general strategies for organizing code and functionality to help with concerns such as maintainability, performance, scalability, and security.

They include sections on abstracting the functionality of the app, the business logic behind it all, a backend/server discussion, and a look at n-Tier architectures from a scalability/performance standpoint...