When I am around and can check on the cups I do not add any water to the bottom of the cup. During the day I keep the cups exposed to air. I will add water in the cup if the air is low in humidity. At night I tuck them in bed into a gallon sized ziploc bag. The bag keeps them moist and a little warmer than room temperature I think.
Once their cotyledons start to open, I'll plant them in that same plastic cup and they stay in it until I an ready to plant outside.
The Japanese do a similar way, that's how I learned what I do.
