Having multiple controller files gives you the ability to organize your code and URLs and it works nicely. To hide the app name and/or controller name, look at the router.example.py file.
All the code in all the files in the "models" directory is executed on each page request so you can put your code anywhere. The model files are executed in alphabetical order and there are a few things that need to be processed in order (which is why you will frequently see model files pre-pended with 1_, 2_, etc as another poster pointed out). If you add a model file, make sure the db.py file takes precedent since it has some code that needs to be run first. You could put all your model information into a file named models.py or you could create individual model files for each table...your preference. It'e pretty easy to re-arrange things so don't get too hung up in the beginning.
