Hi Josh, I don't draw on my lines with pen, I draw on it with pencil once its transferred which some people say isn't ideal since it's too light, I don't think so but I suppose it's a personal preference. If heard people using gouache (which washes off with water) to lighten the surface and then draw over it to make the lines darker. Anyway, I then spray it with some hairspray to seal it so that it doesn't rub off. As far as I'm aware, this doesn't leave lines on the print. You could also try spraying the pen with hairspray but I don't know how well that will work. I think you'll just have to try it out!
Hope this help, do tell me how you get on.
Will Baker Illustrator