Cleaning up my messy code

I am working on a fairly large scale (for myself anyway) project using PHP and MySQL. I am victim of teaching myself to program, not separating presentation from my code-- all the things that lead to masses of spaghetti code so atrocious even I can't figure out what I was doing an hour ago. I'm not looking for an IDE or code generator so much as some practical advice for organization and framework when developing a larger app. I know of PHP Fusebox, having programmed with Cold Fusion fusebox for a while, but it seems like that might be too much. Maybe I just need a sensical, practical approach to application layout. What do you all do? How can I learn to be a better PHP programmer in this regard? c