I have used a fabulous pen that I bought at my LQS. It's made by PILOT and is call FriXion Ball and it comes in different colors. All depends on the color of your fabric, so that the ink will show. After you sew...you just iron and it's gone! I love this pen! I have used it to draw around cookie cutters for motifs on quilts. I have not had any problem using this pen.
Hope this helps you.