Fact of the matter is that most of the time you always have a bunch of existing files from frameworks, CMS etc. from which you develop your project. For that you click menu File->New Project (Yes it is hiding in there!) and select PHP in the Categories section and PHP Application with Existing Sources from Projects sections as shown in the below screenshot.
To ignore folders (normally files folder with images,pdfs etc) from indexing
Goto Project Properties folder and add folders to ignored folders section and save.
Thats it, you can start your project now. Happy Coding!