The" clear coat" would protect the entire finish. As you are proposing two different coatings on top of each other, this would" seal" the deal. A glossy finish used as a substrate for the second step would not be as good, because shiny surfaces are less adhesive to anything painted on top.
Paint the wood with flat black, let dry. It might be a better /thicker coating to use a compatible "Paint" sharpie rather than a regular one for the second step..
As a last step, you can coat EVERYTHING with the clear. As this comes in BOTH a "Glossy" or "satin" finish, it can either appear Glossy or semi gloss. The "Gloss" (shiny) may be less prone to catch dirt, but can also show more surface "scuffs" later on.
Both would seal the project, but it would be your choice.
Finally, determine if this project is intended for Interior or Exterior. Your paints chosen accordingly. Good luck.
