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Ok i think i'm getting this. i don't know that i can work this out though so the pump pumps from the negative edge yet still
cycles through the full water column. my instinct tells me it would just circulate surface water.
That’s the trade off of a skimmer of any kind—skimmer box, intake bay, negative edge, etc. They are drawing surface water.
If you want to circulate the full water column, you will need to add another circulation feature like a bottom drain, jets, or a powerful waterfall falling into deep water.