Where can I learn how to run software?

So I know how to program, and I understand how to write modules/classes hid implementation to control complexity, using layers of abstraction. I start with web development mostly writing PHP and doing back end development. Now I’m interested in Software in general and not being limited to the web. I enjoy writing Python code during my free time because I don’t have to worry about a UI, I can just open a text editor and write code. Lately I’ve been thinking about how to run that code, how it should be bootstrapped. All I really know is to have 1 file like main.py and include all the modules there, create an instance of a class and call methods from the instance. Idk if there is a better way to think about how the software should run as a system? Can anyone recommend any resources?