I'm not overly creative myself, so I usually use stencils. Much easier in the long run IMO. When I mark the top, I have evolved to using just a #2 mechanical pencil on the lighter fabrics and a Bohin mechanicl 'pencil' with a white lead for darker fabrics. I think I have bought every 'quilters marking' pencil on the market and don't like them. I also have and will use the chalk 'mechanical-style' markers as well. I have never had an issue with any of these markers washing out of my fabrics. For straight lines, I usually use a ruler to draw the lines. My friend uses pieces of masking or painters tape. I'm not fond of that process but it works for her. Marking PENS scare me. Have never used any and have no desire to!
I would think that anything that you place on top of your quilt and then need to sew through would be painful. And for the most part, I mark as I go. Particularly with the white pencil. It usually takes me a while to get larger projects hand quilted and I find that the markings will rub off with time and movement of the project. I quilt while watching TV with DH so I have a little 'lap desk' that I place under the quilt to give me a solid surface to work on and just trace as I get to any given area.