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.
Thats amazing! I would have thought a redunancy for sure; in case the right cocpit is unable to operate, fly it from the left if the system is otherwise still oprable.