Oops, now what do I do?!!

"Before I put the big girls in chicken jail, they were living in the new coop and one night, everyone went to bed in the there...little girls included, In the morning when I opened up."

If you can in your neighborhood (not sure if you are trying to control noise or something) make sure you have the coop open Before the chickens get up if you are integrating birds, even one at a time. It is normal chicken behavior for new birds to get picked on when in an enclosed area, (coop), even if they were fine together the evening before putting themselves to bed and running around together the whole day.
If it were me I would just leave both coops open, leave the girls run the yard with each other. Feed and everything in the new coop. Since you have the young birds in the new coop now, as long as they are not trapped in there with each other (youngsters can get away) they should all adjust.
I actually find it easier/faster to introduce more than one bird at a time, it spreads the picking on the new guy around. What you are describing is pretty normal behavior for a dominant hen, she is just establishing her place at the top of the pecking order, there is a reason it is called the pecking order :) Once she feels happy that all the new teenage girls are properly respectful of her, she should stop it. Think about it from the dominant girls point of view, she had a nice happy life, in charge of everybody else, everyone knew their place everything went her way and everybody listened to her ... then all of a sudden a bunch of teenagers show up, she tries to create order in the chaos, they don't listen to her and they won't go away.
Once the new girls are more grown up, 6-7 months seems to be a magic age for some reason, I would expect them to get along with each other. When I leave mine just integrate on their own, it does seem to have something to do with maturity and when they start laying eggs, usually they will be accepted by the new hens around then.
With your dominant hen ... if I understand you correctly, she is a RIR, that does worry me, there is the bad possibility that you just have an overly aggressive hen which is always going to be a problem with other hens/chickens in general, space, age, numbers, nothing matters, they just won't tolerate most other birds around, I have had those, and they were almost all RIR, they just seem to be more likely to be problem hens... but as long as she is good with the two that are her age, I would hope she should eventually feel she has whipped the youngsters into shape and coexist with them more peaceably.
 
I just went through this. Luckily things have gotten better as the young ones have gotten bigger and bolder. I was shocked that my sweet loving Sussex turned out to be the devil in disguise! Even now (it's been 2 months) I can see her evil come out and she chases them off when they dare to come try to hang out with the 3 big girls. After hearing about hens killing new girls, I feel very lucky that it never amounted to more than pulled feathers.
 

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