You can use sheets of flexible plastic or card board temporarily while you pour and shape the substrates, then pull them carefully. You might even be able to leave them in during the fill up then pull them after half full and add the rocks, it'll be a bit cloudy for rock placement right away though. Without a good barrier in place at first, it's likely that you'll get tons of unwanted mixing right off the bat. And be extremely careful filling or the same thing can happen instantaneously when too much water rushes in. Some people set a plate on the substrate to distribute the water slowly, I put the garden hose on trickle and let the water pour down my driftwood. It took a long time to fill so I watched a movie. water clarity is much better when you fill that slow.
In my case, my rocks were quite big and created a thick heavy barrier which was all I needed. Eventually the subs will mix but you can siphon off the top and dust it over with new sand every so often. I use a small hand held kitchen strainer to sift SMS chunks out of the sand.
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