I have done it both ways. I have found that when marking with either the disappearing blue/purple pen or my new favorites, Crayola Ultra Clean markers, it is slightly easier to mark the top before layering because I am only working with the top & can maneuver it much easier than a sandwich; I also can lay it completely flat to trace straight lines with my ruler/straight edge. That said, I have seen videos of brilliant, award winning quilters who even waited until after their quilt was pin basted before they marked it. So ... to each their own. There really isn't one right way.