Those hatcheries can be a real pain. If at all possible use the frozen brine shrimp. My puffer fish loves that.
But if you want to hatch your own, the best thing i've heard to use is a coke bottle. The little plastic ones, not the bit 2 liter ones.
But anyway, fill it with water, and only about a teasponful of the shrimp eggs. Stand it upside down on its cap, and wait for the eggs to hatch.
After they hatch turn the bottle rightside up, and take off the cap. Then get your brine shrimp net and stand over a sink. Then slowly poor the bottle out in the net, and the net will catch the shrimp and the water will pour through.
This has worked the best for me. Just make sure you don't put in to many eggs because a lot of them won't hatch, and when you go to pour them into your net, you'll get a lot of eggs and they will make your tank dirty.