Since nobody really answered it, and I figured it out. I will just answer my own question as the reference for others who might be having the same problem.
I found it easier to use Mongoengine Authentication backend on top of Django authentication. Use the following in settings.py.
AUTHENTICATION_BACKENDS = (
'mongoengine.django.auth.MongoEngineBackend',
)
SESSION_ENGINE = 'mongoengine.django.sessions'
https://mongoengine-odm.readthedocs.org/en/latest/django.html
Apart from that you use pretty much the same code as in regular django, and a bit different at accessing the user from request. Just need to:
from mongoengine.django.auth import User
And if you use form in django, you probably end up using form for mongodb instead. https://github.com/jschrewe/django-mongodbforms