Fungus gnats are a common indoor problem, and the answer is to water the plants with a mosquito dunk liquid before you have any gnats. Or sometimes marketed as "mosquito bits" these can just be dug into the soil or sprinkled on top right from the get go - that way you have BTi leaching into the mix every time you water. It is most effective against only one of the developmental stages of the gnats, which is hard to time if you wait until you know you have a problem. I used the mosquito bits this year for my peppers, and no root devouring gnats this time! (Aphids is another question.. sadly.)
Good luck with your grow, hope you post some more pics as it goes along.
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