You didn't say what you're trying to mark. If it is straight lines across the quilt you can use painter's tape or contact sticky shelf liner. Don't leave them for a long time though.
When I just want to make a tiny dot or so on a quilt I use the water soluble blue fabric pens or tailor's chalk. The chalk should come out completely although you may have to brush it to completely "erase" it if it's a high contract color to the fabric. Use a brush that has a little stiffness to it - kind of like the brushes they sell for cleaning the bobbin area of your sewing machine.