You're almost asking for computer science theory in an easy to read book. If it was that simple, I'd think there'd be more people jumping into the coding scene.
I don't have any recommendations, especially in PHP. There's project design approaches, but I haven't gotten that far into the computer science degree to get to learn about them (I'm positive they're coming up though). You could try finding one of these books, but one question would be would it still apply to coding a PHP site? Maybe. Maybe not.
One thing I can leave you with: divide and conquer. Determine the problem you want to solve. Is it too big? Divide it again. Is it too big? If yes, divide it again (rinse and repeat) Can you directly solve the problem? If yes, you've conquered. If no, keep dividing.
Some people have to write out the notes to the program they wish to create. Others can juggle it all in their head. If you're starting out, I'd recommend jotting as much down on paper as you can. Focus on the unknowns or the "show stoppers" as I like to call them (they're the ones where if they don't work, your app is toast).
As I reread your comments, it might just be a matter of program organization and how to handle all the files. This tends to take practice with the particular language and what works best for you. If this is the case, download a bunch of large scale PHP apps and check out how those coders setup the files and directories and how they called those files.