I’m still not clear on what you have done. You haven’t shown the actual directories involved or the commands you’ve run to create these, or the full layout of your project.
The best that I can do at this point is refer you to Is the structure of the project correct? - #2 by KenWhitesell, where I describe in general what a typical directory structure for a Django project looks like.
As long as your project has a layout comparable to what I’m showing, then your project is ok.
Technically, the virutual environment is not part of your project. Your project runs inside the virtual environment, not the reverse. (For more on this see the thread at Django project within virtual environment or shared common folder)
You can create the virtual environment inside your project directory (the top-level directory), but you will want it to have a different name than the inner project directory that contains your settings file.