NETTUTS.com has posted a few suggestions as to how you can organize your future PHP projects "the right way" and make them easier to maintain.
When starting out with PHP, it can be daunting figuring out how best to organize a project. If you've ever been confused with where to put your images, external libraries, or keeping your logic separate from your layout, then check out these tips; they'll get you heading in the right direction.
The tips include suggestions on things like the directory structure, a project-wide configuration file, creating the simple layout and templating code and an idea to use symlinks to point your web server to the most current directory for your code.