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Stallions don't get a bonus, so can keep them in your barns and show them. :D A mare has a certain range that she can breed from. In any regular breeding, she'll pick a random point on her spectrum. The more bonus a mare gets, the higher within her range of breeding she'll produce. It sort of raises her floor until she's taken out of pasture again. :)

Big stables can leave mares and a stud in their own personal pastures each, but most people don't have the space. What I do is label each stallion a letter, and then match the mares to each stallion. I label them right after their generation name so that when the list sorts them alphabetically, they sort by generation first, and then stud groups. I keep everyone I can in pasture, and when I'm ready to breed, I move whichever group into an empty pasture and breed them one at a time. :)
Getting an email every time you bred your pastures was nice as it gave me a Best out of Each Group, but now you have to prioritize and pick your best pasture to breed first. :)

Let us know if you have any more questions! :D