You have the advantage here that the larvae are generally interesting in eating live food so the eggs are less appealing to them. I've never had any issues with unhatched eggs or shells. My collection method is similar to the above but I keep a lamp with a 40 watt bulb right next to my hatchery (an inverted 1 liter soda bottle). This accomplishes two things - (1.) it keeps the water warm and (b.) it attracts the nauplii. About 24 hours after I have set up the hatchery the eggs have mostly hatched and the nauplii have gathered in the area of the brightest light. I try to keep the brightest light located at about the center of the bottle. This attracts the swimming nauplii away from the unhatched eggs and shells. I turn off the aerator and allow the eggs and shells to either float to the top or settle to the bottom. I then use a pipette (miniature turkey baster) or siphon to suck up just the brine shrimp. I rinse these in fresh water before feeding them to my larvae. Since I keep my larvae in individual 1 liter tubs I just squirt some near each larva. I do this twice a day. I try not to put too many nauplii in at a time since they don't live for very long in the fresh water.