Well my advice for you is to use MVC and a PHP framework.
This will let you focus more on developing the application itself rather than the basic setting up of the project structure.
I use Zend framework and it's great. The only drawback is its steep learning curve and awkward documentation. However, it has the biggest library of classes I have ever seen.
If you feel intimidated by the complexity of Zend framework then you can try CodeIgniter which has the best documentation out there in addition to many video tutorials. These tutorials got me to understand MVC in action.
When you get comfortable with it maybe you can move to a more full stack framework such as Symfony or CakePHP.
Some will argue that frameworks such as Zend, Symfony and CakePHP are overkill for a simple application, but it all depends on goal. If you just wanna build the application fast and dirty make some scripts and it will work fine.
However, if you really want to learn good OO design practices and deep knowledge from some of the top frameworks out there the go for the kill :)