You have (at least) two options:
1) Turn the pen to its final dimensions, sand, finish, assemble, and send the completed pen out for engraving. CA finish works well for this application.
2) Turn the pen barrel a little bit proud of the finial diameter. Send just the barrel out for engraving. Upon return, sand, finish, and assemble.
There are advantages and disadvantages to each method. What you want engraved may lead you to one or the other. I'd suggest you pick someone to do the engraving for you, and discuss with them what works best for your particular cirucmstance. There are several penturners here who do custom engraving (myself included), or you may want to develop a relationship with a local trophy shop.
Regards,
Eric