How do I draw on .pdf with Apple pencil?

Strangely, I was initially able to draw on an iBook with my Pencil, only to have the icon disappear later that same day.

Un-pairing and then re-pairing my Pencil (Settings > Bluetooth, tap your Pencil; then when you’re done, plug it back into your iPad to re-pair) seems to have cleared it back up for me; the icon has re-appeared in iBooks.

Download an app called Notability. You can then send documents to Notability. Once they are in there, you can mark it up. It's awesome!!!!

Do the markups save consistently? My problem is that every time I click Done, only the most recent markup is saved - everything else disappears. Sometimes I don't even click Done - it just jumps to another spot in the PDF and everything I was working on is gone when I go back.