We ususally remove the hen from the nest and put her out to do her scratching and dusting. They usually sit on the floor for a minute or two and then run outside. But doing it this way means you about need two people because to get it dark enough to candle you need someone to hold a towel up to block light so it is dark enough to see.
Option 2 (which we've also done without trouble) is to wait till later at night after it is fully dark and the hen house is quiet. Then just slip them out from under her one or two at a time and check them. Just mark them as they are checked.
Either way would work, deciding factor would be your hen's personality and your coop set up.
