From contributing to Stepmania:

git pull --rebase upstream master
git push origin master
# delete local branch
git branch -d foo/bar
# delete remote branch
git push origin --delete foo/bar
# updating personal fork
git pull --rebase upstream master # pull most recent changes from project.
                                  # --rebase avoids merge commit.
                                  # only drop in case of merge conflict.
                                  # requires setting upstream to stepmania and being on origin.

# submitting a PR
  create new branch
  commit changes to new branch
  push to remote (fork)
  click green "submit pull request"

the branch element is important - PR's are branch based, not snapshots. further commits on a branch that is PR'd will create problems - they'll be part of the same PR.
>> two simultaneous PR's will cause problems.