You do as you would in any other language or any other enviornment.
There are a couple of simple steps in project development:
Organization; You need to organize everything, having documentation, uml diagrams and other pre-work done, before you start programming.
Structure; Before you start coding and also aftter starting, you need to have a focus on structure, meaning that you always need to do it correctly and not do any spagetthi solutions. Keep code simple and well commented.
These two points, are simple and apply in all development areas, despite the language. Keep it simple and well documented and you will find that developing a large scale web app in PHP is as easy as it would be in ASP.NET, Ruby or whatever.
However when we come to the development stage, you need to get a nice IDE, use a good database, use a repo., get an MVC / Template system, this runs in the "Structure"-part though.
Just as a side point, splitting the application into different layers: DLF ( Data, Logic, Front ). Use at least these three layers and you will find that the development will go easy.
