Something that concerns me about marking the top before layering is that sometimes I want to iron the top, especially when layering batting and backing with washable school glue. I like to use my iron to set the glue and get a smooth surface. For that, I'd want to mark after layering. Also, if I mark a border and then want to do any ironing while applying the binding (depending of the method I'm using) I could set the markings with the heat since the quilt hasn't been washed yet. So I think you might find youself using a variety of methods depending on the project.