I would leave a space between the DSB "tray" and the benthic zone (egg-crate). This will allow for water flow, and room to exchange your sand as needed.
If you can fit the sand bed somewhere else in the system, like the unused space at the bottom of an overflow box, you could expand the benthic zone. You could even place the sand bed below the benthic zone if you can squeeze a 4" DSB, 4" benthic zone, and a 4" refugium into your 12". We'll just have to call it a triplex. If you go this route, I strongly recommend making each zone removable, for servicing. Not that you need to do much, but you don't want to paint yourself into a corner.
If you want to feed the sand bed a carbon source or sulphur, you could add a perforated PVC pipe as a "feeding tube". I was able to fit 15 gallons of sand in this overflow. The tank is 4' high, and the VDSB is 24" deep with a feeding tube that goes to the bottom.
At this point in time, I Don't know which is more efficient for filtration & feeding - sand beds, turf scrubbers, or benthic zones. Certainly they all have their merits as "green solutions" for waste reduction and removal. Nature requires all three methods, and it's still a delicate balance, so I don't expect to do any better.
If you think it through, you can find enough real estate for each, without compromising the other. I give them equal amounts of space for now. At some point in time, I'll start "unplugging" each zone, one at a time, to see which has the greatest impact. Then I can size them accordingly.
I use mangroves in my refugium, even though they've fallen out of fashion due to slow growth rates. They do still grow, and permanently remove organics in the process. Their root network grows quite large if they're planted in the egg-crate with "free" roots. Plants are limited to the size of their root mass, perhaps something missed by the hobby as we jammed them in small pots full of aragonite. Zooplankton lives within these "free-range" roots, and I'm sure there are other unknown benefits (phytochemicals) of having these semi-terrestrial contributors. It's all part of replicating a higher ecosystem in our closed systems.
I grow my mangrove pods in soil for six months to get a good head start. If you use dolomite in the soil, you can provide them with enough magnesium. They adapt to immersion quite well, as they've evolved to this process for millions of years. You might be able to plant a few mangroves in your Aquafuge and illuminate them with the display lighting. This may diffuse the light too much for the phytoplankton, apart from the obvious photo-period difference. Phytoplankton will grow better if illuminated from the side of the Aquafuge, as the top is quite narrow for a deep container; although, You may not have room for this option.
