Our company offers coops and runs; however I also love Premier 1 Fencing and refer people there a lot. One suggestion Premier recommends with the electric fences is to keep it more in the open rather than under trees or shelters....
Great things to think about from not only the size of your yard, but also how much time do you want to invest in this... Check it out -
http://www.bestofcluck.com/blog/5-things-to-consider-before-getting-a-coop/
I would design it on paper, with 2 separate entrance doors, a solid partition (just in case they don't like each other!) and just dream up the best of both worlds. On the left chickens with nest boxes, run ---- ...