Sorry if the title is confusing.
What I am trying to say is this: I have worked with Python before, but I'm by no means an expert. So far everything I have done has just been 'somefile.py' with lots of methods and code in it, but it doesn't really have any organizational structure. In Java (which I am more familiar with than Python), there are usually different classes that each have methods and are called from each other. How do you make a file full of code organized and structured when working on a large project? Break them up into files by class?
Hopefully this is clearer. Let me know if this needs clarification.
In Python, the file unit is called module. Modules are organized in packages.
You usually put your classes each in a module and also use modules to group related code that doesn't belong to any class. Related modules are grouped in packages (physically represented by directories) which effectively create namespaces.
Then you use the import command to import the desired pieces of the code into other modules.
You can read about modules, packages and import in the Python documentation here.
Logically, it isn't much different than Java or other languages.