I would like to start development on a web application but really have no idea how to do it. I like to think that I am pretty well versed in PHP, but feel like my coding practices are off. What I would like to know is, what is "the best" way, or a way that you have found to work for you for writing a powerful web application in PHP? I have read about Zend Framework and tried to follow a fairly simple tutorial using it. It seems pretty powerful, but it can be somewhat confusing.
I guess what I'm really asking is how do I come up with the structure of my code? For instance, I have customized this script in the past to fit my needs, http://www.evolt.org/node/60265, and it's very useful and the file structure and so forth makes sense to me, but I just have no idea how they came up with it. Is there somewhere I can read to figure this out?