The roots will seach out the water. Also, when you water from the bottom, it wicks up to the top. If you leave the pots in there long enough the top will be wet as well even in about a n in of water, but I take them out before then. Like Zander said, about 75% is better. It takes some practice to get it down though.
I bottom water all the babies, but when they are bigger, I top water the fertilizer, and bottom water inbetween feedings. I have a large rectangular 41 qt rubbermaid tote that is only about 4or 5 inches deep. It is perfect to fill half way with water and set a tray of plants in. I check the weight every 5 minutes or so until they feel heavy then take them out.
jacob