Acrylic paint would be one method, as David noted. You can also get archival, artist marker sets. I've got a set of 20 from Staedtler. Any decent art supply store should carry something like that. They can work well. Unlike with paints, you can't mix colours.
The other thing to consider is that any areas you fix after the fact won't be covered with whatever topcoating protectant you use. Since the areas are small it shouldn't be a big problem but it's something to keep in mind.
You might look at a different method of packing and transporting your pieces as well, just so that these kinds of problems are minimised or eliminated.