Both ends of the U tube have to stay submerged at all times in order to maintain the siphon. Fill both boxes with water, insert the air line tube up into the U tube, all the way to the highest point, and SUCK!
Sorry...
You'll suck all the air out and the U tube will fill with water and the water level will drop until the level in the skimmer box equals the height of the baffle wall in the outside box.