There's a chaos theory behind these things. Organisms will thrive in the right conditions and parish in the wrong ones, thus segregating the various zones of your naturalized filtration system. Your idea is a three level ecosystem.
- nitrifying bacteria lives on the detritus on the rock, in an aerobic environment (top)
- benthic invertebrates, such as copepods, sponges, tunicates and worms live on the underside of the rock, where it's dark and flow is minimal (middle)
- denitrifying bacteria lives in the sand, in dark anaerobic conditions (bottom)
That's how it works in nature, so you shouldn't have a problem. Everybody knows where they belong, and what their job is.
Having said that, you can fine tune each zone to increase efficiency, kind of like an assembly line.
- copepods will flourish in a refugium with macro-algae
- nitrate and phosphate removing benthic invertebrates will excel if they are given more surface area, such as egg-crate panels
- a DSB will be more efficient if it is isolated from detritus build-up, rather than allowing it to become a settling point at the bottom of your sump
Each zone requires different lighting, flow and water quality. You can allow nature to take its' course and settle with what it gives you, or you can harness the power by manipulating each zone for maximum efficiency.
You already have a good head start by having a large sump to display tank ratio.
