Suggestions for Separating and Reintegrating Breeding Groups?

I have 3 different breeds with 5 different colors. I have 2 to 5 roosters for each. Which are usually at different stages of maturity.

My bantam flocks are smaller.(in number, not just size) So I have 2 to 4 mature roosters of each breed or color. My Barnevelder flock has 100 hens so I run 10 roosters with them. Plus 4 in reserve. I have a bachelor coop also. My coops and runs allow plenty of space. Plus when I am not collecting hatching eggs. Most everyone gets out to free range every afternoon.
Do you let the different flocks forage together? I have four different coops with separate attached runs and rotate which of the four groups I let free range for the day. Ages from four months to two plus years. One group is mostly Silkies. Have more than one rooster in each group.
 
Do you let the different flocks forage together? I have four different coops with separate attached runs and rotate which of the four groups I let free range for the day. Ages from four months to two plus years. One group is mostly Silkies. Have more than one rooster in each group.
I do the same thing with 5 coops as letting more then one out the males will fight
 
Let me try to summarize. You have one Black Langshan and two Blue Australorp roosters. You are thinking of getting a Blue Cuckoo Marans boy next year.

You want to make black sex links with Cuckoo Marans and Dominique girls. And you have some Blue Australorp girls you want to mate with Blue Australorp boys only.

Blue is a modifier of black. That means your Australorp boys and the Blue Cuckoo have a black base, the Cuckoo also has barring. You can use your Australorp boys to make Black Sex Links with those girls. You cannot use the Cuckoo because he has barring. You don't need the Langshan to make sex links, but if your personal preference is to hatch some of his kids, so be it.

Maybe I'll need to breed Blue Australorps and buy chicks of other breeds to keep some flock and egg color variety (should sell better than all one color).
To get various egg color get different hens and hatch various egg colors. You can do which breeds should lay which colors and shades as well as I can.

Since Blue is based on black and black is so dominant if you use Blue or Black roosters practically everything you hatch the first generation will be black or blue (with or without barring). No real feather color variation. If you want a flock that has a variety of colors get a red or buff rooster. This allows the color of the mother's feathers to have a lot of influence on what the chick looks like. I'd stay away from a white boy, you don't know what is hiding under there if it is Recessive White, and if it is Dominant White you have black hiding under there.

I'm collecting data now and will surely change my practices with experience. :D
To get what you want you have to know what you want. And you are right, as you go through this that will change. I like simplicity and I like flexibility. You work so you won't always have lots of time to get too complicated. I also like sufficient room. I think you need to start designing how you can add a separate coop and run and keep the feeding, watering, and other stuff close together. Your comfort and convenience are two of the most important components in this.

As ambitious as you are I'm not sure how many built-in brooders or broody busters you need. I'd try to design them to be multifunctional. Brooder, broody buster, isolate a chicken, isolate rowdy cockerels, and for a broody hen, either incubating or raising chicks if you separate your broodies. Yeah, your plans will change as you go along and get experience. And I can help confuse you.
 
My suggestion would be to let the roosters continue to co-exist within the flock.
Put the hens that you wish to collect eggs from in a see-don't-touch coop and run. Each evening put the selected rooster in with them and release only the rooster into the flock mid morning.
 

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