Mark it lightly, but make sure it can be seen by the typist. On one page items, paper clip the shelflist card to the item. All others should be inserted into the item. If so, mark the title page instead of the cover and put a post-it note on the cover alerting the typist to the fact that you have marked the title page. If you don't do this the typist is likely to type the individual title just from habit.
International series have a numbered series card as well as having an individual shelflist typed.
You will recognize these in the shelflist. As you run across them, it might be a good idea to also make that note on the Roladex card for that series. If it is in the middle of a title, you can use arrows to indicate to the typists that this should be skipped. If you want the department as well as the agency on the shelflist, mark both with slashes. It may be unecessary to have both, because many agencies within departments have an identity of their own and can stand alone.