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AFAIK the display order in the file navigator panel (any of them – Project, Project Files, etc.) is not arbitrarily user-selectable.
To avoid the confusion it would probably be a better idea to actually split your django projects into separate PyCharm projects – what you have right now is just a single PyCharm project which contains files spread across multiple directories. The split will also save you trouble down the road by preventing potential conflicts between your projects.
With separate PyCharm projects there is no room for such confusion as each project is open in its own window (even when chosing to re-use the Pycharm window the existing project is closed when a new one opens). From Opening, Reopening and Closing Projects doc section:
PyCharm allows opening several projects simultaneously in different
windows. By default, each time you open a project while another one is
opened, PyCharm prompts you to choose whether to open the project in
the same window or in a new window. If necessary, you can change this
behavior using controls on the System Settings page.In the Project Opening section of this page, you can choose one of
the following options:
- Open project in a new window to open a new PyCharm window each time a new project is opened.
- Open project in the same window to stay in the same PyCharm window.
- Confirm window to open project in to keep the default behavior and display a dialog box to choose how to open each new project.
You might want to scan through the entire Creating and Managing Projects chapter and/or the Creating and managing Django project tutorial.