As your other post seems to be closed to comment I shall have to reply here.
You obviously don't have a cogging problem, I think you are confusing cogging with the drag on load.
I suspect your alternator is reasonably efficient if you can light two 50W bulbs easily by hand. I think your 40W output is likely to be the limit of the water wheel rather than the alternator.
At best all you will gain with a dual rotor air gap design is the elimination of iron loss which in your case is probably small and the effect mostly bothers wind turbines on start up. With constant water power you may only gain a few %.
If you make it dual rotor you will need more magnet and copper to reach the same efficiency and even more to bring the efficiency up enough to compensate for the iron loss.
If you want the highest possible efficiency regardless of cost then the dual rotor should do best but it may not be the most economic commercial design.
I assume you have looked at matching the alternator to the wheel, if you have too little open circuit volts or too much resistance you may not be fully loading the wheel. Have you checked the power direct into lamps, which you can keep adding until you slow the wheel to where water spills over the buckets.
If you know the flow of water you can easily calculate the power out, you can take 75% for wheel efficiency and you will be lucky to exceed that on the alternator unless it is a monster with lots of magnets.
Flux