There are lots of different ways to achieve this. Some information that might help you plan. It takes an egg about 25 hours to go through the hen’s internal egg making factory. That egg can only be fertilized during the first few minutes of that journey. So if a mating takes place on a Monday, Monday’s egg cannot possibly be fertile. Tuesday’s egg might be, depending in when the mating took place and when the egg started that journey. I would not expect it to be. But Wednesday’s egg will be fertile after a successful Monday mating. Of course, this is after a mating. A rooster does not necessarily mate with every hen in his flock every day, but he doesn’t have to to keep them fertile.
Right after the mating takes place, the hen stands up, fluffs her feathers, and shakes. This fluffy shake moves the rooster’s sperm to a container right where the egg starts its journey. The sperm can last for quite a while. Most of us count on a hen laying fertile eggs for about two weeks after a mating. A few can even lay fertile eggs for more than three weeks after a mating. So if you want to clean out a hen from an old rooster and make sure the new rooster is the father, you need to keep the hen separated from the old rooster for at least three weeks, maybe a few days more. It doesn’t matter if the new rooster is with the hen or not. What matters is that the old rooster is kept separate.
There is a twist on this. A poultry science professor at the University of Arkansas said that the special container that holds the sperm operates on a last in – first out basis. That means that the last rooster to mate with the hen will be the father of the chicks. I trust him but that doesn’t mean you have to. You might want to wait the three to four weeks for the hen to clean up. With the eggs I have in the incubator right now, I removed the two roosters I did not want to be the father on a Monday and started saving eggs on Friday.
Do you only have one rooster? If so, keep them all together and separate the rooster and the hens you want to hatch from when you are ready so you know which hens have laid those eggs. That way the rooster never needs to be alone.
If you have more than one rooster, you can approach it different ways. You can keep a bachelor pad. Keep only roosters in there together. No hens allowed. You can keep one rooster with the flock if you want with all the other roosters in that bachelor pen. Then swap the rooster’s out as necessary to get the right hens fertile by the right rooster, isolating hens and roosters as you need to so you can meet your goals.
One rooster will be OK in a pen by himself. He won’t like it but he won’t go into a depression and commit suicide. He’ll want out. He’ll probably spend a lot of time pacing the fence, looking for a way out to join the flock. You don’t have to pipe in reruns of Dr. Phil or Oprah to help him work out his inner conflicts. He’ll be OK but he won’t be happy with or without those reruns.
Or you can keep all roosters with the flock and remove the right rooster and hens as required. One problem with this is the roosters will almost certainly fight when you put them back with the flock after the roosters have been separated. Usually these fights are fairly serious but they usually work out which one is boss and get over it. Occasionally it is as fight to the death or serious injury. One really huge factor in this is how much room you have. If the loser has plenty of room to run away and get away when the winner is chasing him, it normally works out. But if space is tight, it is a lot more dangerous. I don’t know how big your pen is, but it sounds like you could have some risks here.
Breeders often keep one or two hens in a pen with one rooster throughout the breeding season and don’t have issues with over-mating or anything like that. There is a secret to that though. They don’t use adolescents. They use mature chickens, male and female. Adolescents have hormones running wild and have not worked out the techniques to mating. They don’t understand the part they need to play, pullets as well as cockerels. Mature chickens have learned to control their hormones and know how to play their part.
I don’t know your set-up or how many hens and roosters you have and how you want to sort them. It’s probably not going to be possible to have just one pen during breeding season at least. Maybe you can work something out for that when you are not in the breeding season. Good luck with it.
Hens go broody when you don’t want them to… and won’t go broody when you do. 
