I MUCH prefer to remove the air line after hatchout, let sit for 4 minutes, and siphon off the nauplii into an ice cream container. Then I pour through the mesh to capture the nauplii, rinse to remove all traces of hatching water, and then add to the grow out container. If not using decapped cysts then I also treat with a 5 minute hydrogen peroxide bath before the rinse.
Remember, they can't feed on the greenwater until they are about a day old when the molt into instar II stage. This means you will end up with exoskeletons in the container that many people think are dying nauplii. Roughly speaking they will go through about 15 of these molts by the time they mature.
These molts are another reason for cleanout of the containers as the food settles and decays and the molts decay along with nauplii feces decaying, providing perfect conditions for nasty bacteria to thrive. Usually when a brownish tinge starts to the water it indicates the molts and feces have decayed.