iWhen I first started, I was advised to move the hen and eggs to another place, she sat there 3 days, left and went back to her old place, those eggs died, and I remember my grandfather telling me that a cow knew more about being a cow than he ever would, and I applied the same idea to chickens.
I let her do what she wants to do. Granted, not every chick will live, but they often times don't when you incubate them either. If the hen lives with the flock, she will get down, once a day or two, take care of her needs, stomp around, growl at everyone and go back to her nest. This makes her quite high in the pecking order, the others give her a wide berth. Which when the chicks hatch is good, cause the chicks will stay close to her, and the layers secretly wonder just what the broody hen did, but whatever, and leave them all alone, and get used to them, and the flock integrates themselves.
Where people get into huge problems is, they separate the hen away from the flock. The flock forgets this hen. Then the hen hatches the chicks, and they are so tiny and fragile, that they keep them away from the flock until they get about 4 week old, and want the flock to be a flock again. They put the whole group back into the pen, the layers attack the strange chicken, and the broody hens hormones are dropping, she no longer defends her chicks, she is trying to defend herself, and the layers often times kills the chicks.
Marking the eggs is a good plan, because when the hen is out, some of those layers will sneak in and lay an egg with the idea, "hey, you may as well do all the work for me too!" Then the nest gets too filled with eggs. The eggs are in different stages of development, so would hatch at different times in an incubator, but the hen will leave the unhatched eggs. Every two or three days, take a towel down, and CAREFULLY lift her off the nest, checking carefully under her wings. She will peck at you, so the towel will protect you from that. That way you can see what eggs are under her.
I have had them set perfectly for weeks, and then, get on the wrong nest! Ugh! But not to worry, just move her back. The eggs had been without her for 4-5 hours (estimate) and were cool to the touch, but hatched right on schedule. After the first few days, the eggs themselves produce some heat.
Good luck, there is no better way to raise chicks than with a broody hen, I will never go back to a brooder box, what a mess.