One thing that I've found quite confuddling about the workflow at the moment is what the best way of managing groups of layers - while you can move around individual material layers, duplicate them etc. folders seem to be a bit of a black hole. You can't duplicate a folder and, if you place a layer into a folder, I can't…
You can move layers out of folders by ungrouping them. Holding down the "Alt-key" while clicking the "Group button" will ungroup the folder that is currently selected! Duplicating folders is something the dev team is looking in to at the moment! Let me know if you have any further questions!