I was in the similar situation that you are need now when my chicks were getting older. My solution was that I set up a temporary fence inside my run to split the birds. Once I did that and they got a little older, they learned that they could fly over the temp. fence, but couldn't get back into their pen. I then mad a hole in the fence for the little birds could go through, but not the larger birds. This made it where I could keep feeding them their grower until they were 18 weeks old (recommendation from Purena). Also, I keep meds in their water and if you give it to the larger birds, you have to discard their eggs.
As Far as nesting boxes, I was only going to have 4 boxes but my wife talked me into building 8 of them. I only have 13 hens which 4 boxes would have been okay. Now that they are all laying, they use 6 of the 8 boxes, so I am glad that my wife talked me into it.
some older pictures of my coop can be seen on my BYC page for ideas.
