This is an excellent article explaining all the ins and outs of designing your coop and run:
http://naturalchickenkeeping.blogspot.co.nz/2013/04/how-much-coop-and-run-space-do-i-need.html
When you do eventually integrate your two flocks I've always had great success keeping them side by side...
If you are doubling your run size it sounds like a good amount of space for 9 chickens. It's likely, given the conditions you describe, that the chicks weren't being fed properly. Low protein intake can lead to chicks taking to each other, feather picking which can lead to bloodshed. I'd really...