Really you only want to water the plant for its size.. if it's a seedling.. obviously you won't need to water the entire pot fully. A consistantly wet atmosphere around the seedling can cause Damping-off as well as other things like mold/fungus.

Water for the size of the plant, not the size of the pot.

For the first few days.. up to a week.. you'll need to water.. either every other day.. or daily depending on lights,temp, ventilation..