I bet it would work but it would be cloudy for a while. If you could get the fish to one side of the tank with a divider so they wouldn't get whomped with air. Do 3/4 of the tank with underwater system and use the divider to keep the fish on the safe side. Or do half and half. two separate systems on each half and clean one side at a time so the fish don't get their ass kiked with air.
If your running the dual overflow like you made keep the divider in until the water clears on one side.
If your running the dual overflow like you made keep the divider in until the water clears on one side.