It really depends on the size of your waterers. I don't use marbles because I use quail waterers for the first two weeks. If the water is more than an inch deep, I think I would keep the marbles in. If it isn't as deep, I'd probably take them out about now.
I think what I am using now is between one half to one inch deep. When they begin to go outside I will make sure it is not much deeper than an inch ...at least for a while. In another week and a half I think I will give her the option to take them outside as long as the weather cooperates.
Thank you.