To make a PR when you already have a fork of vanilla PS:
Locally, add PuzzleScript Plus as an origin in your PuzzleScript repository.
Fetch and check out a branch from PuzzleScript Plus (likely develop unless instructed otherwise).
Now you can commit there, push it, and use that branch for PRs!
It's not made clear that you have to first push a PR branch to your own fork, and then raise the PR from your fork to PS+.
The steps I suggest are:
Develop your changes locally, using either a clone of PS+ or a branch checked out from PS+.
Locally, make both your fork and PS+ remotes of your local repo.
Commit your changes locally onto a new branch that will become the PR. Give it a nice name including 'pr' and the issue number eg pr-psplus-#9999
The README says:
It's not made clear that you have to first push a PR branch to your own fork, and then raise the PR from your fork to PS+.
The steps I suggest are:
pr-psplus-#9999