Nichole, do a treatment to the soil you are going to pot into - I zap the soil in the microwave, so, you ad very little water to that mix and allow it to cool off covered with a fabric or something that breathes, but won't permit any possible snicky one in that soil... then when cup is ready to be removed, soak in water water with mosquito dunk in it... you will have to soak to loose the roots from the cup, might as well give them something that if gnat comes to eat, it will not taste so good to them.
Upon transplanting, do not water anymore than what you already did to remove them from the cups. Here in our area, they do not need any more water than that, and less water, less tempting soil for these nasty creatures. I had a few outside that had nice sprouts in early fall, I just check them...an whoolah...all eaten up! they are everywhere outthere...everywhere, I just never noticed them before. That is whey they spray fruit trees...they are evil, once the plant is strong, they can eat away, the plant will survive... Upon digging my large tree roots for my experiments, I see damaged roots there also... an my chickens come crazy to scratch to eat them. they are great in compost piles. I guess it is the cycle of life.