I would recommend perlite because I have found that it kills fungus gnats. I had a lot of them from using unsterilized soil and they were killing seedlings, which are very vulnerable to the larvae eating their roots until they flop over and die. So I tried perlite for the seedlings instead of soil, using some hydro fertilizer. It worked perfectly. I can actually see the dead fly bodies on top of the perlite. It appears that they get cut up on the sharp edges of the perlite, like with diatomaceous earth, and die from drying out or whatever. Diatomaceous earth is too fine a dust and is just a mess to use and the dust is harmful to the lungs and virtually impossible to prevent getting stirred up into the air and then as soon as you water it it washes away so perlite is much better. Perlite is basically glass that's puffed up with air and has a lot of little sharp edges. I haven't even seen one gnat crawl down through it. They just sit on top. The perlite dust is bad for the lungs too though so you should poke some holes in the bottom of the bag and pour water in it to get it wet and rinse out some of the dust before you start putting it in the pots, or don't even poke the holes if you don't want a mess of water running out. I don't know if it would be good for filling in your watering depressions or not because it would probably move around a lot itself when you throw water on it. Maybe a layer of perlite followed by a layer of Hydroton. That would still stop the gnats getting to the roots.
