IT IS NOT RECOMMENDED to allow hatch water to come into contact with the system water. Cysts harbour nasty bacteria that can, at worst case scenario, wipe out your tank contents.
While some get away with it, to me, it's not worth the risk with the money I have tied up in my tanks.
Brine Shrimp Direct has a note on their site regarding this point, and it is also noted in the article on Artemia in the UN's Live Food For Aquacuture.
Personally, I stick a piece of rigid air line tubing into standard air line tubing, and place it in an inverted 2L pop bottle with the bottom cut out, and sitting in the bottom that is cut off another bottle.
After hatchout, I siphon off the nauplii from between the top and bottom crap, rinse with fresh water, and then use as required.
To make use of the excellent fatty acid content, they should be fed to the target as soon as they hatch out.
Better yet, is to decapp the cysts with bleach and then either use normally or just add the decapped cysts to the tank where they can be eaten before hatchout when nutrient value immediately starts to decline.
RAISING BRINE SHRIMP TO ADULT BRINE SHRIMP DIRECT CLICK HERE AND SCROLL DOWN TO SECTION 4.0, ARTEMIA