I'm not sure what your best plan of action is because the flock dynamics provide too many variables without knowing them.... but I can tell you that we usually give our hens 2 or 3 days of peace and quiet with there new hatched chicks and then they are able to go into the main coop with them, but in the main coop they are given a quiet corner where they can retreat to when things get too busy for them. A broody hen usually is quite effective at protecting her little ones though if she is low on the pecking order or a banty size who is outmatched by the other hens in the flock then you will want to supervise for a while.... you can also provide food behind a fence that only the little ones can fit through so they can eat without being harassed by older birds. (a piece of 2x3 or 2x4 goat type fencing would work) or cover their food dish with a fence hood and elevate it 3 or 4 inches off of the ground so only the chicks can 'creep' under it to get to their food. If you search for 'creep feeders' on this site you will probably find some picture examples of them.
Before you place the chicks in the main coop you should give it a good once over with an eye toward potential chick hazards.... they are experts at getting stuck in cracks and crevices or falling into areas they then can't get out of. Either my DH or I do head counts every evening and usually during the day also. Any time I see a broody out and about I count how many are with her and if the count comes up short I start looking. That is pretty simple unless you have multiple broodies which routinely share chicks, but that is a different situation.
Besides their creep feeder and a safe haven for them you will want to make sure they can easily reach the food and water which is out for the other birds. I usually just use a block of wood or a brick as a step in front of the feeder or waterer. Even when they have their own places to eat or drink they like to imitate the older birds.
Thanks for letting me know about the food and water situation. I had made a creep feeder last year when I had chicks with a 5 week age difference. I have 2 nipple waters that are identical that I am using one for them now and I can set them at different levels but still put a step up for the other one. I have a feeling that Anastasia will do a fine job of protecting them. She was kind of a loner before but nobody bothered her. I think I may just go with the dog crate where they can huddle at night or during the day if needed but otherwise be with the flock. I do need to do some spring cleaning and safety measures in the coop before I make the move. I even impressed that she takes them down the ramp of the broody coop/run in the morning and back up at night. They have just done so well I hope it keeps up.
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