I see two main options: designated virtual lanes that are programmed into drone navigational systems, and robust sense and avoid systems that allow seemingly chaotic pathing to remain reasonably safe. In practice there will probably be a combination of the two.

As for who decides what the rules are, well, in the US it's pretty easy to predict that the FAA or perhaps some yet-unconceived federal agency will try its best to strictly regulate commercial drones, and will probably largely succeed at least in crowded areas. I have my doubts that it's the best possible way to organize the activity, but it's the most likely.