The good code starts with order IMHO.
If the project is so small there's virtually no need for multiple files, then there's probably no need for php either.
If there's a need for php, always use multiple files.
Store the program, the settings, function libraries, classes, the templates (layouts) all in separate files. If there's more, then keep them separated by theme as well.
Edit: you might want to allow the non-templated versions sometimes, where the layout and the base programming is virtually one. Other stuff still goes outside.
Don't be the programmer everyone uses only once and the just wants to forget.
Lazyness is an ugly excuse for this kind of slackness 🙂