I have 5 cockerels among my free range flock. And to be honest, they seem to have sorted themselves out, and have "their" hens. The older bantam cockerel is in charge of the top half of the field, although the other hens go up there, he will not allow the other cockerels. Never fights them, just chases them back into their bit of field. I have only ever seen him tread the 5 banties he is housed with.
The main flock, including the ex batts, are looked after by Les and Mike, the two Pekin boys - bottom half of the field though. The silkie cockerel, has his silkie hens, and is chased by Les and Mike, and the bantam cockerel, so knows his place. One of this years clutch is a cockerel, and he has not got his own ladies as yet, just drifts around
Thats just my set up, and as far as I can see, as yet, no one is interbreeding, although this years bantam pullets could be a problem in that respect.
The only way round it is to pen up the ones you wish to breed from, so they do not mingle with their relations.