Thanks for your insight. However giving the chance since i have not flooded the tank i m thinking to dig up some soil at the back and put up a barrier between the soil n vent (a mesh with rock perhaps) to allow water to flow. I am also concern about dead zone if solely rely on the upper intake.Flourite Black Sand? If so, it's ultimately going to get mixed in with the Amazonia over time. Which won't really be a problem - just be prepared. And Amazonia won't break down as quickly as you think it will.
The lower intake on the Flex is there to prevent filter burnout if you allow the water level to drop below the upper intake, so you shouldn't have a problem. You could seal it up entirely if you wanted. Just be sure to do top-offs so you still have water flow into the filter compartment.