Use a Wax Crayon, they are made in many color's.
So matching the color isn't a problem.
You fill the hole and level it off.
Use a padding lacquer over the hole.
For larger hole's use wood fill or a burn in stick.
If you use a wood fill, you will have to sand it level, stain the fill to match the color.
Use a padding lacquer over the fill area.
You may have to apply the padding lacquer over the whole surface.