I have very recently bought an iPad Pro 12.9" and an Apple Pencil. My basic aim was to read books and write notes on the book while I read. This is what I have learnt:
1. I had created many documents in Microsoft Word and Pages on my Mac Book Pro and had later saved these in pdf format. I copied these pdf documents to my iPad Pro using AirDrop. When I open these documents in iPad Pro, a circular pencil tip symbol appears in the right upper corner of the document, clicking on which enables me to write on the document with Apple Pencil and my finger as well.
2. I am learning Arabic language and have downloaded some free pdf books and video lectures on the subject. I wanted to take notes on the pdf book while listening to the video. Initially I could not do that. With trial and error, I learnt that if I first make the pdf book 'editable' it was then possible to write on its pages as I have described above in para 1.
3. This is how I converted my pdf book in to an editable document. I opened the pdf book on my Mac Book Pro using 'Preview'. On the top part of the screen, I found a pen tool with an arrow to open a drop-down manue. While I clicked on it, a message appeared that my original document was not editable therefore an editable copy has been created. I was able to locate that copy next to where I had saved the original book. I copied that editable pdf book to my iPad Pro and was delighted to find that it was possible to write on the pages of that book as well.