best practices for moving Pycharm proj to production?

When I run my program direct from the command line there are issues with imports failing. This is because the subdirectories that were identified as source in Settings>Project Structure are not in sys.path. I have solved them by adding python code in the script to add the directories to the sys.path. Is there a better way to deal with this issue? Are there other issues to consider when preparing a project to run without starting it in PyCharm?