5/16 (or 8mm) is what I use. I found the ones shorter than that are too short to even go through the seat base. You will see it takes a very powewrful stapler to make a good job.
Make sure you put lots of downward pressure on the front of the stapler. I use two hands - one to pull the trigger, and the other one on the top of the stapler pushing down. This eliminates any kickback and lets the full force of the shot go towards sinking the staple.