The way I understand it, you have isolated the broody and her eggs so the others cannot get to her nest. There is no need to mark the eggs now that the others cannot get to the nest. Marking the eggs I want her to hatch and removing any other eggs daily is how I handle a broody hen that is not isolated from the flock. By the way, I hope all the eggs were started together. If not you have a staggered hatch which is a problem.
The other hens will settle down. Where they wind up laying their eggs I don’t know. It could be another of your nests or just about anywhere else. They are creatures of habit and often hate change. But they are also adaptable and they will adapt. I suggest putting fake eggs in your other nests and try to keep any eggs not in a nest picked up to help guide them to another nest.
Different people handle broodies different ways. I don’t isolate my broody hens from the rest of the flock either as they lay or as they hatch and have never had a problem with another hen laying with the chicks as they hatch. They will often lay with the broody before hatch starts. One time I had another broody hen fight with the broody over her eggs as they were hatching. The second broody heard the chicks peeping and wanted them for herself. Some eggs were destroyed, so yes there can be a risk. Other than that one time I’ve never lost a chick to another adult when they were hatching or while the broody was raising them with the flock. I’ve never had a hen that failed to protect her chicks from another hen if that was required no matter what her position is in the pecking order. I know others have had problems with that. You are dealing with living animals and anything can happen.
For your first time especially and until you actually see a broody hen in action, isolating the chicks as they hatch is a reasonable precaution. We are just strangers on the internet often offering conflicting information. Who do you believe? A warning. If you are isolating the broody make sure the chicks cannot get through the wire or out of that isolation. My flock very seldom bothers chicks on their own, even very young chicks, but a chick where Mama cannot protect it is at risk, either from the other hens or something else. Make sure those chicks cannot get away from Mama’s protection. That’s one of the risks of trying to isolate them, you fail to really isolate.
Some people isolate the hen and chicks until the hen weans them or even longer. Then they are faced with an integration. I prefer the broody hen raise the chicks with the flock so she handles integration for me. I’ve had a broody wean her chicks as early as three weeks, though that is pretty unusual. Somewhere between four and nine weeks is more normal for me but some take even longer than that.
Isolating a broody and her just-hatched chicks where the rest of the flock can see them isn’t a bad thing. It gives the chicks a better chance to get mobile and to learn to eat and drink without interference from the other adults, plus it gives the hen and her chicks a better chance to bond and the hen a chance to teach them to obey her. I generally don’t do it that way, just let the hen bring the chicks off the nest whenever she is ready an let her handle everything with no interference from me, but it’s still a reasonable thing to do. But I want her to still be in full broody protective mode when the chicks are introduced to the flock. If she hatched where the flock can see her and has been isolated with the chicks where the flock can see her, she probably will have no reintegration issues herself. If she is some mysterious hen they’ve forgotten about that suddenly shows up with a bunch of chicks, she might or might not have her own reintegration issues.
A good rooster protects all members of his flock. Some roosters are better than others, but normally if the new chicks are introduced to him at a fairly young age, he assumes they are his. Sometimes a dominant rooster will help a broody hen take care of her chicks, especially if there is some problem. Helping does not always happen, but I have never had a dominant rooster threaten any young chick. Most of my hens don’t threaten a young chick either unless that chick wanders into their personal space, though occasionally some will. That’s when Mama kicks butt.
A story I like to tell and I’ve seen this many times. I’ve seen a two week old chick leave Mama’s protection and go stand next to the other adult hens at the feeder. Sometimes the other hens ignore that chick, at least for a while, but it usually doesn’t take long for one of the hens to peck that chick to remind it that it is bad chicken etiquette for that chick to eat with its betters. After that peck the chick goes running back to Mama as fast as it can run, peeping and with its little wings flapping. Mama ignores all this. That chick needs to learn. But if the hen that pecked the chick starts to follow it (usually they don’t but it has happened) Mama gets all upset and whips butt. You might be able to discipline my chick but you sure can’t threaten it.
There are lots of different ways to do any of this. They all have their benefits but also their potential drawbacks. Our individual experiences will guide us in what we do. With practically anything to do with chickens, there is hardly ever one way that is right for each of us where every other way is wrong. There are a lot of different things that can work with their own benefits and drawbacks. You’ll develop your own methods and style as you go. Welcome to the adventure of broody hens. It can be a fun ride.