I had a bad gnat problem stemming from (un)happy frog last spring. It manifested slowly through veg, and got real bad just before I wanted to flip to flower. I tried a number of things, and eventually used a multi pronged approach to knock them back. It was a war, and very frustrating, but it worked - over time. I refused to use bt toxin or toxic pesticides of any kind.
Plants were in 5gal felt bags. I started by drying the soil out thoroughly (about 7-8 days without water), I then used the shop-vac to remove all the loose soil from the top and sides of the containers, right down to the root ball. I fully topped the containers with fresh soil mix (rice hulls and Stonington), and worked it down the sides of the pots as best I could. The top dressing was about 2 1/2 " when I finished. I watered it in with a strong water / neem oil solution (I think it was 6tbl concentrate : 1 gal water - it was in the pamphlet on the side of the concentrate bottle).
I set up a yellow sticky trap in each pot, and hung a couple of fly strips in my tent. (Vinegar traps will catch a few, but nothing compared to the sticky traps, and they stink too). After two days, I watered with a hydrogen peroxide solution (3 water : 1 Peroxide), and sprayed the top of the soil with neem oil solution - smaller ratio of neem oil in the spray). BTW, the plants LOVED the peroxide soak and it really aerates the soil!
Then I alternated feeding waterings and peroxide soaks for the next two weeks (3 total peroxide soaks), ALWAYS spraying the soil surface and base of the trunks with neem oil solution after every watering, trying to deter the adult bugs from entering the soil. I've heard that a little peppermint oil can be added to the neem oil solution too, but I didn't have any.
This method assaulted the infestation in five ways. 1) It took out a majority of the nesters and larva in the loose soil when I got rid of the loose stuff. 2) It put a major deterrent (neem oil) through the soil and all over the root ball in the initial soak. 3) The peroxide soaks worked on killing the larva without toxins (over time). 4) The neem oil sprays deterred re-entry of adults flying around. 5) the sticky traps catch the flyers over time, reducing the number of egg-layers getting to the soil.
I eventually destroyed them, but it took even longer than the initial two week treatment to knock them out. They are really hard to get rid of once established. Prior to this, I tried several of these things, and others, individually, with no success. I firmly believe it took the full combination of methods to truly do the trick. Good luck!
PS - I never buy Fox Farm anymore.
I treat my potting mix with boiling water before planting, problem solved, but it's a PITA. 
