You have the watering understood correctly. The soil won't wick completely to the top, but it will get close. I planted my seeds in rapid rooters so all I had to do was touch to the top to see how moist/dry it was. I did this in veg, but i no longer am now for flower. I now water from the top and I just get it to drop a little bit out the bottom. The last two waterings I have used 1 gallon water for all the plants each time. I probably had about 2-6 oz of run off that I just waste.
Use the bottom watering for seedlings/vegative and it'll be impossible to over water them so you'll be able to learn just how much they use.
The problem with the paint chipping off the rubbermaids can be easily corrected by first spraying with a special primer made for plastics.