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Do a project!
Once you got the coding down, everything else is just details. Typically you learn those things by experience. The thing is that every environment and project is different. There is no standard way of setting up a project. A lot of people use common structures (etc, lib, src, bin), but other than that, each project is very different.
There are thousands of libraries, the vast majority of which you will never hear of or need to know. For example, a popular library on Linux is gtk and there are many more. But anything you learn with gtk will not carry over into the windows API. You have a project you want to do, you do research to find what libraries will be helpful, and then you learn about how to use them through online documentation.
I will soon be getting my associates in computer science.