I don’t have a complete answer to your question, but I can point you to a few resources that might help you get started. I’d definitely suggest reaching out to the authors of the paper you cited. It does sound like they used manual fiducial markers of some type. I’d be curious what those markers were specifically (maybe I missed it, but they didn’t seem to specify), and also how they made the transformation from stereotactic coordinates (assuming that’s the known coordinate system of their fiducial markers) into CCF coordinates.
Here’s a Jupyter notebook that shows some basics for accessing structure masks and other functions in the CCF:
And here are two potentially useful representations of the top down projection:
Hopefully that’s helpful in getting started. Feel free to post back here with follow-up questions as you make progress.