When you upgrade from the Qualified Crew Course to the Skipper course, the system recognizes you have already purchased the crew course and so will upgrade you for the difference in price. Just sign-in and go to purchase the skipper course. The difference in price will be automatically calculated so that you don't pay the full price. You're Welcome!
(This is the case for the Skipper course - not the Skipper Small Keelboat Course)