Markup with Apple Pencil in split view watching video

I was watching a video lecture in split screen and trying to use the Apple Pencil to take notes in the provided PDF handout (Books). Apple Pencil did not work, I could use my finger however (scrawling, not writing).

a) is there a way to get Apple Pencil to work?

b) if not, do you have a suggestion for a workaround? (No, I'm not taking notes elsewhere and transfer them later. Yes, I could watch the lecture on my iPhone and annotate on my iPad. Better suggestions?)

iPad Pro 12.9" (2020), Apple Pencil, YouTube, Books