Actually B and C are identical. It doesn't matter where you run the pipe between the pump and where the first output is.
The higher you pump, the less performance you will get out of your Hammerhead pump. B and C will flow slightly better than A because water is allowed to exit before being pumped up higher. In A, all of the water has to be pumped up to the max height.
Reguardless, you are going to have to valve the system. Each tank will need a valve to control the flow. The bottom tanks need to be valved so some of the water will be pushed up to the upper tanks. The upper tanks still need valves since there are two on top. If the feed pipes are not perfectly level, most or all of the water will go to just one top tank.