For the Wet/Dry part you should have the bioballs, or whatever, out of the water for best effectiveness. Unless you have a high fish load, leaving them submerged will cause no harm. The point of the Wet/Dry filter was to have high stocking levels of critters before people figured out that whole live rock thing in reefs. Wet/Dry was adapted from the water treatment industry where speed/economy of space/cost/time was required.
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