For those who breed - what's your setup?

The problem with keeping any chooks separate from any others is that the hierarchy must be resettled every single time you reintroduce them. Some will do this with a scuffle or two, a couple of boots, others will harm or kill. It's worse when introducing adults who have been reared separately. Males and females will fight one another too if normally they are kept apart so have no understanding of the natural separation of their genders' hierarchies. Alpha roosters don't have to battle hens to take that role, they battle males, and the same is true for alpha hens not having to battle the other gender for their status, but when you keep them apart they can come to view the other gender as being the same as their own since they've always lived in a unigender world.

There are more often than not serious social issues created by only briefly and suddenly introducing genders to one another and keeping them separate in the meanwhile. The positive social behaviors of a rooster, and the hens' perception of, and response to them, are in large part learned and this learning is naturally gained from hatching onwards if raised in mixed gender groups. The same applies to the males. Mating is only part of their natural social interaction; the rest, for a rooster, involves finding food, finding nests and even making nests, guarding hens from predators, and other behaviors including in some individuals paternal instinct which can involve trying to brood eggs, snuggling chicks, feeding them, etc, but the paternal instincts in particular most males lack.

Mating is the strongest instinct there so it's often retained when all other social interaction instincts are lost, but if all your roosters do is mate with hens in a frenzy when introduced for a short period every few months, the chances of damage to the hens are much higher as they often lack a positive association to the males so they're often scared or uncooperative and the over-excitement and lack of experience on the males' parts only reinforces that negative response. After all in such circumstances the male is only a temporary and often aggressive strange bird who appears, wreaks havoc, and then disappears again for weeks or months at a time, no trust or positive associations are established, no social bonds as is natural to the species. Normally a rooster 'woos' a hen before attempting to mate, and bad first impressions can be permanent. If hens get into the habit of panicking and running whenever they see a rooster, there's a chance they'll never take to them and the roosters can also fail to behave calmly if their mating opportunities/time with hens is so limited that there is no time for natural social bonding.

Males reared with only males also tend to exhibit mixed aggression and reproductive instinct and savage hens while mating, because in all probability in his mind he's merely mating another rooster again. In all domestic species you can foster stressful, damaging, fatal, and all-round abnormal gender relations (both same-gender and other-gender) by practicing complete lifelong gender segregation except for brief mating times.

Also the hens may completely lack interest in the roosters and having to endure living with them can be traumatic and damaging to them though a good rooster can usually bring such hens around so to speak.

Introducing the genders for only short periods can lead to learned rooster aversion in hens who otherwise would have welcomed the presence of a mate and all that entails if they'd grown up with the other gender. This can negatively reinforce aggressive and brutal tendencies any rooster may already have present, and such tendencies are usually exacerbated by the gender segregation he's been reared with. Those roosters without such tendencies won't be a problem but rearing has a lot to do with it, and there's many good and bad roosters out there so it's hit and miss unless you've been selecting them for generations and rearing them under conditions that enable positive social behaviors to be predominant.

Hens also may show heightened aggression due to the lack of males, and some hens may mate other hens and conflict with roosters as they view them as other hens. These sorts of issues are commonly found in stock from backgrounds where they've been kept and reared without natural family units, so they've had their instinct made dormant by lack of stimulation of it, and loss of ability to act on it and thus reinforce it, which indicates that it's an obsolete instinct when in fact it's still necessary for anyone not running a factory or totally segregated setup. Any chooks from backgrounds that involved routine artificial incubation, gender segregation, AI, etc can generally be counted on to demonstrate social dysfunction which can lead to extreme stress and deaths.

For a peaceful flock you need to rear them at the very least in separate family groups involving both genders and ideally their chicks together, or all in one group, with sufficient nutrition and stimuli and space, and ideally cull against excessive aggression since retraining is often a fools' errand as it's got a strong genetic basis. Retraining can work but it's very unreliable and almost all lapse sooner or later, and retraining one individual doesn't remove their genetic bias towards aggression and it's risky both for you and the rest of the flock to try to breed it out, which takes up to 7 generations... On that note, good records are very beneficial to keep, you'll often need to refer to them, especially when you least expect it.

I keep my males and females all together, and chicks are reared among the main flock too, and have separated pairs or trios etc for breeding when I wanted to ensure offspring from those specific individuals, but I make sure they remain very visible to the main flock if segregated so they're not forgotten and this reduces conflict when they're released again. But generally, because I have so many family lines, I just let them breed as a main flock and continually remove individuals from any generation who are mentally or physically or socially unfit. But I'm breeding mongrels and for dual purpose freerange traits, not to any S.O.P., so my methods and objectives are very different to someone breeding showbirds or purebreds for example.

Tendencies towards violence, whether male-male, male-female, female-female, or female/male-chick, are strongly heritable and can easily be culled and bred against. If you have bully issues it pays to not get rid of the victim like many do, but get rid of the bully.

Best wishes.