I plant 3 seeds per cup of the same cross. I always like to hold back a couple of seeds in the refrigerator .... just in case. I have had the roots get really dense in the cups, but was able to divide them and transplant them up into their own pot or into the ground in the Spring. But I can plant mine early because of the zone I live in, so growing them in 12 oz. cups has not really been a problem for me.
The gnats on the other hand are a real pain!!! So bottom watering should help control the gnats?