I end up adding:
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "mysite.settings")
not only to my manage.py file, but also in the app files where I was calling 'setup_environ'. So, I replace this code:
from django.core.management import setup_environ
from mysite import settings
setup_environ(settings)
with:
os.environ.setdefault("DJANGO_SETTINGS_MODULE", "mysite.settings")
No DeprecationWarning and seems like its working!