Depends on what your soil contains, I would say if they look good leave them be. As far as fungus gnats that is a widely discussed topic here, tons of different methods. What has worked for me is 1 cup of 3% h2o2 to a gallon of water, soak the soil pretty good, let it dry completely, one more dose of the h2o2 and water and let it dry, then go back to normal water. Oh and fly traps to nab the adults buzzing around.