I use the template method too. Not having the exact fit hasnt been much of a problem. The over spray that gets on the rubber part is hardly noticable, especially after the weathering is done.
I did try the Sharpie way too. I was using a brand new marker, and it just seemed to dry out on the tip as I was (painting) with it. Ive tried it numerous times, with different markers and it just seems to keep drying out the tip. I know, its a simple task, drawing with a pen, but what am I doing wrong? I have the same problem with my fine tip pen when drawing in panel lines on a/c.