I have the same aragonite sand in my tank and its all settled, it moves around and i push it back once in a while, i have a 3k+gph powerhead blowing around in my tank with a 1200gph return pump and a 900gph powerhead all blowing around in there. But if you are still having issues, i agree, get some crushed coral and throw it on top/mix it in. As far as substrate getting caught under layers, i wouldnt worry too much about it, as long as you get some sand sifting snails and starfish, they will help keep it stirred up and bacteria will break the rest down. Certain fish like small Gobies, even horseshoe crabs do better with finer sand IMO.
With the aragonite, it took a while for my tank to clear up, i'd like to say less than a week and several sock changes during that week (sometimes twice a day but usually once a day). The scrubber isnt needed right now but it doesnt hurt anything, it's roll will be of better use when you get some fish in there and have to feed every day, though the high spikes in ammonia and Phosphates will help the screen develop.