I put the empty supers under the full supers. By keeping empty space above the brood nest you suppress the urge to swarm.
Generally a good rule when adding drawn comb however having a box with undrawn will likely not affect the swarm impulse or so I've read. Perhaps someone with better knowledge will expound. Many will suggest that adding the super above the brood nest will not keep a hive from swarming and I am inclined to believe this. I doubt it will make a difference but if I were in your position I'd switch things and make the partially filled super #1 above the brood boxes, make #2 the full super and add the empty box on top-there is still plenty of room in box #2