Granting that the article is by CNN, I read it to mean that each cockpit has a set of controls, but only one is in command during a flight.
OK, I didn't want to click on CNN, but I read an article somewhere else that said that one side was basically just a shell for carrying more fuel tank capacity, and didn't have anything behind the cockpit windows.
According to the Wikipedia page on Stratolaunch:
The pilot, co-pilot and flight engineer will be in the right fuselage cockpit, while the left fuselage one is empty and unpressurized. The flight data systems are in the left fuselage.