Nobody really answered this question for you but you have probably figured it out by now. If you are going to separate them, you need to keep them separate all the time. Otherwise you would have the logistics of trying to round them up and put them in the appropriare pens morning and evening, and what a fiasco THAT would be! You'd just need a bachelor pen where the boys live together all the time, away from the girls. But why? What use are they to you? You'd just be feeding them for no good reason. Better to rehome* all three, or rehome two and pick one to keep that you and the hens can live with.
*Rehome or put to other good use. My feeling is, if I'm going to eat chicken (and I do), I'd rather eat home-grown, healthy birds I raised myself.