The marks from a Sharpie don't seem to soak into the wood that much. It can easily be sanded off. I usually mark just outside the length I need, cut just inside the mark, then sand to get that "perfect" fit.
I'm getting ready to cover a Sig Rascal with transparent orange Monokote so, no marks allowed! And yeah, after using yellow Ultracote on a G.P. Skybolt, I've sworn off yellow altogether.
Hey, has anybody figured out how to get paint to adhere to Monokote? I would prefer to completely cover the Rascal, then paint on the trim color.