Start by determining in a completely human-centric way (i.e., forget the code for now) what exactly you want the application to do. Jot notes on a napkin, write an outline in MS Word, or use a full-blown requirements analysis tool - how you do it is not as important right now as it is that you think about what needs to happen (or not happen) when someone uses your application.
Once you have a good understanding of what should happen, then you start thinking about how. I usually start at that point with the underlying database design: what data needs to be stored, updated and retrieved. (Now it's time to start reading up on database normalization.)
You might then start roughing out some of the more important front-end portions - the HTML forms that interface with the application - so that you get a handle on what bits of data need to get passed around for things to happen. (Now it's probably time to start reading up on handling form inputs in PHP.)
Then you'll need to dive into the "guts" of the PHP code: validating form inputs, saving results in the database, retrieving data from the database and displaying it, etc. Once again some planning and forethought is beneficial, rather than just diving in an churning out lots of code that you end up scrapping when you realize you're doing something wrong.
