First, always make your pull request in a branch.
Second, when you add some change (in a branch), update your master
branch from the original repo:
git remote add original /url/to/upstream/repo
git fetch original
git checkout master
# make sure you don't have any work in progress
git reset --hard original/master
Then rebase your current fix branch on top of master
:
git checkout fixbranch
git rebase master
You can then push that new branch to your origin
(your fork):
See more with this couple of tips on pull requests.