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That small section in the tank is what is referred to as the baffle area... The purpose is to give the water a chance to have the microbubbles float to the top of the water, and have the water without bubbles flow under another retaining wall...
Generally a refugium has a very slow flowthrough.. This allows the macroalgaes a chance to rid the water of some problem organics and nutrients...
Yes, the bio-balls are a no no in a reef tank.. They are nitrate factories... Unless the rock will be completely submersed in water in the baffle area, I wouldn't do it. LR would be better suited in either the first, or last section or wherever it will be completely submerged...
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