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Watch out for an ammonia spike if the arena sand came with any manure. Especially if it is finely ground. There might also be readily available nitrogen in the soil, too, of course, but the use of 'arena sand' raised a red flag in my mind.

Soil in the sump would be dependent on what plants you want to use. I would use plants that are rooted in the substrate, with leaves above the water, so yes, add soil to the substrate.
In each tank with fish keep the floating or drifting plants. Things like Java Moss, Guppy Grass and similar fine plants will provide a safe haven for the fry, and microorganisms for them to eat when they are newborn, and perhaps too small to eat many prepared foods.

Plants will use fertilizer (AKA remove waste) faster with more light. Even in the shallow set up you are proposing I would try to get more light over the sump, or at least VERY good reflectors to make sure the light you can supply ends up at the plants, and not all over the fish room.
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