We did a similiar set up as well. I had a separate small run for integrating the new gals but they outgrow it too fast ( small backyard) so my idea to DH was to build a "patio home".
The main coop is on the opposite side of the run.
Really love the idea and plan on copying it for my set up. We also have a chair in our run and it's their favorite spot. Sometimes all six somehow get on the chair. As far as the poop, they poop all over it and I just wash it off with the hose.