When the Jetbrains site said one could not use custom settings files with PyCharm, I was concerned; until I realised the comment was more than 2 years old. You CAN use custom settings files.
Basically, you need to manually set the “manage” file to your django-admin.py file, and make the following modification to the additional options. You must also make sure to define the PythonPath within the Environmental variables.
After this, my server ran just fine.