I don't have enough info to help you out there. What Apple pencil do you have? If you have the first generation, then you can plug the pencil into the lightning port of an older 12.9" iPad Pro, but not the most recent generation. If you have the 2nd generation of Apple Pencil, it will charge by magnetically attaching it to the side of the latest iPad pro, but not by plugging it in anywhere.
If you don't have either of those, then you have to charge it using the instructions provided by the manufacturer.