You probably need to add the "upstream" remote yourself. For example, for OI Shopping List:
git clone g...@github.com:my-account/shoppinglist.git shopping
cd shopping
git remote add upstream g...@github.com:openintents/shoppinglist.git
This will make "origin" be your fork, while "upstream" is the OI repo. You will probably need to use "git remote add" even if your initial clone was made with "repo".
Then when you want to update, for example when you are preparing to submit a pull request:
git fetch upstream
git rebase upstream/master
git push -f origin master
-- Aaron