The longer side of the iPad contains magnets as well as Apple's Smart Cover so I made a simple temporarily attachable magnetic dock for the Pencil to carry it with the iPad. 
 I made a shorter (with a single magnet) and a longer version (with 2 magnets). Shorter one works but I think I'll like the longer one more.

The pencil's diameter is 8.9 mm - the tube I have designed is 9.3 mm. Because the magnets sticks to the pencil too they are able to keep the pencil within the tube even in vertical position. 

I suggest to print the mount from ABS and wipe out the magnet container hole with a drop of acetone using a cotton bud. This will make the ABS sticky and the magnets will be fixed inside their chamber without using any additional glue.
Before you fix the magnets inside their chamber try the bare magnets on thelong side of the iPad and let them to align their orientation.