rbblue8:
I'm not trying to be a smart ass, but I don't know how you would expectd anyone here to be able to give you much advice about your project from the information you have provided?
Is it a project that is going to launch a rocket ship to the moon or keep track of a few mp3 songs or what.
Most every project is very unique just as people are unique and unless you fully explain what it is you are trying to do in your project how can anyone make any suggestions for you?
All I can say is that very few projects are contained within one file.
Depending on what you are trying to do your project might need to have a database, header files, footer files, input forms, etc., etc..
I sounds to me like you should either do a Google search on a term such as "Designing PHP Projects" or get a good book about PHP/MYSQL and really study the part that talks about designing a project.
I am sure this probably did not answer your question, but the way you have asked your question it appears impossible to answer.
Good Luck
