I have a rectangular 10G with about 2.5in of Ocean Direct oolithic sandbed. The water pump, hydor koralia 450, is in the middle of the longest glass pane, near the water surface and the live rocks are tightly touching each other and lined up in the middle with no stacking, while leaving open sand space around them. There's a "mountain" rock on each end, and flat rocks in the middle to allow the water flow to pass through with minimal effort. I followed the water flow, via the floating debris. It goes around the rocks and if it hits the glass, the topmost water goes downward then gets picked up by the water current from above, goes topward, then redo the cycle. It looks more complicated but it's just a simplified description.
This is the after the redo of the aquascape. Before I had both ends just get piled up nicely. The koralia is in the same spot. This left the rocks at the end of the water flow with greatly reduced water flow. Never smelled or saw black spots with the rocks in the area with the most water flow