Chris Hartjes' Blog: Organzing Slim Framework Applications
I've never really used a microframework in PHP before. I used Flask for a Python project that I did to experiment with using Google App Engine. The principles seem to be quite similar (although I will admit that having decorators in PHP would be ineresting) but the trade-off with a microframework is that you usually have to figure out an application layout for yourself.
He also uses the Pimple dependency injection container, Twig templating and Composer for package management. He describes how he got it all set up - organizing the code so Composer could understand it, creating the Twig templates directory and creating some of his default routes.