I don't use a case on the 12.9. I felt any of them made a large device even more bulky.
For a pen holder, I use two of these attached to the top edge, You could get by with one, but I found two keeps the pen from swiveling.
It is very sturdy and the pencil holder is snug enough to keep the pencil in and is also magnetic. The case does not interfere at all with the keyboard flap. I have had a lot of people ask me about the case. It looks very slick and professional with the keyboard attached and the white pencil on the side.