x2 on the extra fine point Sharpie, as it will not dent the wood. I use a dab of acrylic paint from your local craft store to cover any marks that might show through to the finish (for example, if you were using yellow film covering which seems to let every underlying imperfection flash through).

I also use Sharpies for any markings on covering material. A dab of alcohol on Q-Tip cleans it away easily.