I assume you are talking about these.
I always start in these or red party cups. Depends on the day. Sometimes I care about the earth and sometimes not. lol
With these, I just bury the whole thing. The red cups obviously I transplant out. Guess you could just cut the bottom out and plant the whole red cup.
Not sure about the over watering part. Depending on the temp, I water the babies every 4-5 days. When they get larger I water every 2 days. (Just dump a gallon of nuted water into each tub) I keep shit real simple. I have an old 10cc syringe that over time the numbers rubbed off. I do a best guess on nutes. It's all good.
If you have 4 plants in a tub like mine, I don't see how you could over water.