Sometimes it is simply faster to mark up a map with what you know–especially when people of the same name are moving around and appearing in a variety of records.
Failing to acknowledge geography can cause problems.
And sometimes it is simply faster to notate in pencil as you are thinking. There will always be time later to make a neat copy if necessary.
Sometimes making a neat copy slows me down and I lose my train of thought.
I always have blank copies of maps on paper so I can start taking notes “geographically” when necessary.