Personally, I would build a separated area. The reason is that I started out with one long run and one big coop. I have been dividing it up because I now want to work on purebred/project birds.
Another reason is that next time you have broodies you can use the separated area to put them in - instead of having more and more eggs collect under them from the laying hens. If you line the smaller pen with the baby chick wire so the chicks can't get into the main pen, and the mommas and chicks can run around together (and the mommas protect their own chicks from other mommas) things will be much less stressful for everybody. If you put the birds that went broody in the smaller coop they will feel comfortable to stay there when (notice not if) they go broody again. Having that pen alongside will allow the integration to go smoothly, once they are big enough to free range together just let them all out.
Right now I have 5 pens. Three pens were made out of that long pen. I let everybody out together to range, and they all go back to the right pens. I can have more roosters, have more choices as to who I put where (growout pen is also bantam pen.. the older birds teach the younger roos manners) and I can switch them around if I want to.
I also have a portable cage I use for my "breeding pens" for the bantams (too small for big ones). I did single pairings (only had pairs) and hatched out purebred chicks to try and get some more females. These are put away when I am finished doing the breeding pens.
The other two pens are for my Silkies - and they share a very small coop in the middle but have long runs on either side of the coop. By doing this I have one coop for two areas - separated in the middle so the birds can keep warm together but not see or bother each other inside. I also divided under the coop into two areas so there is a digging hole area under there - thats the only place the two roosters fence fight - but it is through baby chicken wire so they can't even get their beaks through it.
If I was going to have one layer flock and not care about parentage of the littles and I only wanted one or two roosters - I would still have one big pen and one big coop.
But because my plans changed, thanks to this site and chicken math, I am now going for dividing areas up for less birds per area and more control over who breeds who..
thanks so much for the detail (and thanks to Kim as well) -- this is so helpful in thinking things through! sounds like a separate space would be the best addition at this point. i don't know that i'll be doing any breeding, but it might be nice to have the option... and you're right, that being able to keep broodies in a separate space but without fully separating them from view would be an improvement! good to know that they can free-range together but then go home to separate pens...