I don't think you need to separate the coops at opposite ends of the property. They can be close together. If there are problems with the two roosters fighting, then put something something solid between the two coops so they can't see each other, like ply wood or old tin roofing.
The problems I see with them running together are that the roosters may fight, and the big rooster may try to mate with the silkie hen, which could hurt her. But you'll know more from observing their behavior, so make decisions based on that.