I have 10 hens and they only used 1 box. The other one next to it just sit there and collect dust. I think 3 boxes would be enough for your 12 hens. My suggest would be 1 long box with slot/divider that can make to 2 or 3 boxes if need. I also suggest you make the 1st set little higher and leave enough room below for 2nd set in the future. This way when you end up 30+ chickens and there room to add 3 more boxes down below and able to use the same roof top cover from the 1st set.
Do as you see best but as others have already pointed out, hens have their own opinion as to what constitutes the best, most secure, or comfortable nest.
99.9% of all the nest designs in the Universe are intended to please the human who gathers the eggs usually in a manner that least inconveniences the human owner. That means that no thought what so ever is given to what the hen truly needs, wants, or likes. So as I said, "Do as you see best!"