Depending on the desired outcome, I take two slightly different approaches. If I want just an engraving, then I turn, finish, and assemble the pen as usual. Then, I engrave the letter, name, logo, photo, etc. into the pen. Virtually any color fill can be added and the finished product will have the desired text permanently laser engraved into the the pen.
If I want an inlay (i.e. final product with a smooth surface), then I rough turn the barrel to approximately 1/8" oversize. Next, I will engrave the text, image, logo, etc. Then I will fill that engraving with a contrasting material such as embossing powder, inlace, crushed stone, colored epoxy, another wood, etc. I return to the lathe and turn the barrel to final dimension, sand, apply the finish, and assemble the pen. This will result in a smooth surface with the image in a contrasting material.