Yes, how old are they? That is a big key to their behavior. There are two different things sort of related to age though it is really more maturity than calendar age. Are they laying yet or getting ready to start? If they are getting ready to lay I want them to have access to the nests so they at least have a chance to learn to lay in the nests. That will influence how I manage them. If you were surprised at five being able to crowd into a nest I'd guess Point of Lay age but I don't like to assume. How many birds total, sounds like maybe six?
The other is sleeping behavior. Until they start to roost they like to sleep in a group. They get comfort from being together. To me, roosting means they spend the night on the roosts. I call them playing on the roosts during the day perching. I've had a broody hen take her chicks to the roost at 2 weeks, I've had brooder-raised chicks start roosting as early as 5-1/2 weeks, most tend to roost at 10 to 12 weeks, a few go longer. Even in the same grow-out coop there can be a huge difference in when different broods start roost, but calendar age will at least give us some insight.
Coop configuration can influence where they sleep. Ar your roosts higher than the nests or anywhere else you don't want them to sleep? Do you have adequate roost length and can they get to the roosts? Do you have ramps, steps, or enough room they can spread their wings and fly up and down without banging into things. Some more information or even photos of the inside of your coop might help us understand what is going on. Age, number of chickens, and size of the coop help determine if it is safe to leave them locked in the coop section only during the day.
If they are still pretty young and you don't have any birds laying eggs in that nest, then sleeping in there for now wouldn't bother me that much, I'd just change out clean bedding when I needed to. But I'd probably block off the nest and force them to sleep somewhere else as long as no chicken is laying in that nest or is about to. If they are point of lay, I'd move them to the roosts after dark and make sure the coop is really dark when you do that. They should get the message and start putting themselves to bed on the roosts pretty soon, provided hey are higher than the nests and they have adequate room.
If your chickens are going to free range I'd leave them locked in the coop or coop/run for at least a week. The idea is to teach them that the coop/run is a safe place to spend the night so they will return there at sunset. I'd be even more comfortable if they were roosting and not sleeping in a group on the floor or somewhere as you aren't exactly sure where they will decide to roost, but a week should work a vast majority of the time.
If they are always going to be locked in a coop/run and never free range things change. It's no longer a case where they may just wonder off or start sleeping in trees where you can't find them or get them if you can find them. I've done this several times, both leaving them locked in the coop only and allowing them access to the coop and run from the start.
The main reason you lock them on the coop only is to try to get them to put themselves to bed in the coop section and not the run when you give them access to the run. It's never worked for me but I think my coop configuration is mainly to blame. When I do this they are almost always five weeks old and not yet roosting, that might play a part. With my elevated coop they want to sleep under the pop door instead of going into the coop. I don't have this problem with my coop at ground level. Chicken age, coop/run configuration, and other issues can give us different results.
Whether I leave them locked in the coop only for a week or more they always want to sleep in the run. If I just put them in the coop/run to start they always want to sleep in the run. So at dark, when they have settled in at night and are pretty easy to catch as long as it is fairly dark, I lock them in the coop for the night. My typical brood size is around 20. Sometimes it only takes a few times of locking them in the coop at night for them to get the message and go in on their own. Often it takes about a week before all are going in on their own. One time it took three weeks before the last three decided to quit fighting it and go in on their own.
There can be other reasons to lock them in the coop section only at first. One might be if they are really young you might want them to grow up a bit more before you expose them to the weather outside. I'm sure there can be plenty of other reasons to do this one way or the other. Where you feed and water may influence it. If you only have food or water in the run of course you don't want to lock them away from it during the day. I don't think there is one right way to do this, where every other way is wrong. There are just different ways to go about it.
I you leave them locked in the coop only for while you may be in for a show. When I first open the pop door to give them access to the run, sometimes they are all on the ground in 15 minutes. Sometimes it can take three days before they get brave enough to venture outside. Each brood is different. It can be hilarious watching them go to the pop door, look out (I want to go! I want to go!), but then turn around and say, not yet. I feed and water in both the coop and run so I let them work it out.
