bub cloner: in or over water?

I know that you can do it either way. Either put it in the water, or over the water.

I've been putting them in the water.

I was at the hydro shop today and the guy- who seems to know a lot- said i should put them over the water. he said there would be less chance for rot, and said generally that it was better to put them over the water and let the bubbles pop.

I understand how each method works, but i just wanted to post a general question to everyone:

Do you do over, or in the water?

does anyone have an opinion?

Would anyone like to share how they do it?

Also, how much roots do you guys wait for before planting?

mine are in water but I just made mine. I also have a heater in mine from the aquarium that is submersible. I am planning a monster grow for next season using a garbage can as my dwc and aeroponics.

anyone have any input???

I was really hoping to get a bunch of responses so i could try to figure out which method i should use.