Hello Alexey,
Thanks for contributing!
1. You should make a PR against master and, if you're fixing a Trac ticket, start the commit message with "Fixed #xxxxx -- bla bla bla".
Version indicators such as [2.0.x] are added when patches are backported to stable branches. You don't need to care about this now. If your issue is
eligible for backporting, then the person who merges the patch will likely do the backport as well.
2. Yes, your fork should be up to date with Django's master branch to ensure that the PR is clean.
3. As you wish :-)
I'm not aware of any guidelines about this relatively new GitHub feature when contributing to Django.
Best regards,