Its really just personal preference. I use the 2 Gallons in the Ebb an Flow system and have gotten great results, I am even considering using a few large ones outdoors this year..curious to see if the roots will make there way down into the native soil.
As for my Soil set up I like keeping the roots inside the container..probably just a mixture of my OCD and the fact that I already own a butt load of #7 pots.
I do think you will have great success with them for cuttings and seedlings though and imagine you could almost just sit them into the Auto Pots as soon as there ready as the roots will continue to make there way through. They are very permeable. Good luck with the Pandora's Box, Mine just came in the mail today!!