The Left prong is for priming only. That is, when you set it up or if air gets in the take in tube, plug it on the left (or just clamp the tube) until water rises and fills the chamber.
The right prong is to feed air to the impeller.
My suggestion is to just remove the tube completely. It should run quiter this way and doesnt affect performance unless you're running with ozone accessories. You should be emptying it every other day at least. For best results, ajust so that the level of the water is just under the O-ring. Its one of the best hang on skimmers out there for under $150 and other than the noise it makes, I would keep it.