I always add ground up Bti(Mosquito Dunks) to my soil mixes now. When I first was getting started I got a serious case of fungus gnats and fought them all the way through harvest, I suspected they came from a the premixed soil(roots organic) I was using at the time. If you are already fighting the bastards as seedlings than you have a long road ahead of you but Bti can be used to control them, as with soil drenches of Azamax. I would probably just start over with different soil if it isnt going to be too costly.