Traditionally, I have configured the UWSGI configuration file to call an application like below:
mydirectory/uwsgi_application.ini ... #python module to import a
You don't use Flask-Script with uWSGI. You point it at the app directly. Or in your case, you point it at a call to the app factory. The simplest example is:
uwsgi --module 'myapp:create_app()'