Probably the best way to learn how to structure your program is by reading other people's code, especially if it's a large program to which many people have contributed. After looking at the code of many projects, you should get an idea of what the consensus style should be.
Python, as a language, is special in that there are some strong guidelines as to how you should format your code. The first is the so-called "Zen of Python":
- Beautiful is better than ugly.
- Explicit is better than implicit.
- Simple is better than complex.
- Complex is better than complicated.
- Flat is better than nested.
- Sparse is better than dense.
- Readability counts.
- Special cases aren't special enough to break the rules.
- Although practicality beats purity.
- Errors should never pass silently.
- Unless explicitly silenced.
- In the face of ambiguity, refuse the temptation to guess.
- There should be one-- and preferably only one --obvious way to do it.
- Although that way may not be obvious at first unless you're Dutch.
- Now is better than never.
- Although never is often better than right now.
- If the implementation is hard to explain, it's a bad idea.
- If the implementation is easy to explain, it may be a good idea.
- Namespaces are one honking great idea -- let's do more of those!
On a more practical level, there is PEP8, the style guide for Python.
With those in mind, I would say that your code style doesn't really fit, particularly the nested functions. Find a way to flatten those out, either by using classes or moving them into separate modules. This will make the structure of your program much easier to understand.
