Question: A mutual friend recommended that I ask you for some PHP related help. I haven't had a class so I never learned a way to formally structure my files and folders. Is there a program or method that you would recommend to do this?
In the end, it depends on the architecture of your application, as well as the subtleties of things like the user interface (e.g., primarily mobile or whatever). Based on your site's needs, such as performance and ease of use, you should probably aim towards a more AJAX-driven app so it works more smoothly and efficiently.
So, take a look at some of the links and see which one makes sense to you and seems to fit the vision for what you want to do. Don't take too long, though; to some extent, you won't really know until you try several of them, and it's best to just get started building your app. Whatever you pick, it will work far better than just a chaotic pile of PHP scripts; I've been there and done that, and it gets very messy very quickly!