Hey Jen - I was looking for a similar answer (having a site admin mark courses as complete at the program level, since users would not be enrolled at the course level) and realized you might still be looking for an answer:

Assuming a user has the role you selected (site manager), they would be able to go into the Course Completion Report and see the check box to "give" their approval (I was testing with a role called 'AC Completion test'):