I don't have a logic for this but if the hitter, left or right, is under 5'8 or so I prefer the scissor.
If I'm doing HP 3-4 games in a day I switch between the two. If you do as Umpire In Chief says, base your position on the hitter every time you shouldn't notice much of a difference. This is also good advice because catchers at higher levels move all the time anyways so no use positioning off them.
If you are using the scissors make sure your shoulders and neck are relaxed, this will lessen the impact of foul balls to the mask and fatigue. I have seen guys stick their neck out like a trophy animal mount, they are the ones who get dinged the most in the scissor.
In my opinion too many young and new umpires use the box incorrectly and really should use the scissor until their skills develop. They don't see the outside corner and call too many strikes that are down and or away.