When to bring broody with chicks back with the rest of the flock

[kana9]

I have never hatched chicks before and instead always bought day old chicks, so excuse my inexperience. My Blue Wyandotte hen was sitting on two eggs that have gone through a lot, so I was sure they were not going to hatch. When I had her with the flock, she was sitting in a nest box and when she would leave, other hens would go in her nest. Twice when I went to check on her, the eggs were in the nest empty and cold as the other hen had left, and the broody was sitting on another nest. I moved the hen and eggs into another, adjoining part of the coop, and put the eggs in a new cat litter box with the nest liner in a dog crate. The crate door was open so the broody could come out. After three hours of moving her I came back to check on her, and both eggs were outside the nest and cold. She had actually turned the whole box around to face the other way. I did not see any cracks in the eggs, so I put them back in the nest. She liked that setup and kept sitting on the eggs. Based on my inexperienced eye with candling, I though the eggs were due to hatch on Thursday. I had read here that the broody was not going to leave the nest for the last three days before hatching, so when she was out of the nest twice two days ago, I was sure the eggs were bad. I never heard any sound from her, or the eggs. so, much to my surprise, I first saw a part of an egg shell next to her on the nest this morning, and then two little heads peaking out later today. Still no chirping! My newbie questions are:
1) Are chicks under a broody always quiet?
2) Do I need to remove the cat litter box and just leave the nest liner, because it is about 4 inches tall? Can the chicks get out to the water and starter I set up in the dog crate?
3) How long should I leave the broody hen and her chicks in the separate part of the coop? They can see the other two parts of the coop (the main part with older hens and rooster, and a grow out pen with six 6-week old mail order chicks).
4) Do I need to worry about the rooster with the chicks? The good news is that this hen grew up with the rooster and always hangs out with him.
5) The broody hen is on top of the pecking order with the other hens. Does this mean she will be more successful at protecting her chicks?

Sorry for the long post, and thank you in advance for your help.

 

[AltonaAcres]

In my limited experience, chicks are only loud when cold or distressed, so when under mom they are fairly quiet. I would remove the litter box, and just have them in a pile of straw. Don't change the setup too much though. My broody was sneaky and had chicks without me knowing, so she went in with the flock immediately. I would wait 1-2 weeks based on how everyone's doing. The roo shouldn't bother the chicks, maybe will just be confused. Unless they are in a teeny pen with the roo he won't bother them. A hen will protect her chicks whether she's ruler of the roost or picked on, lowly, one.