Yes, a three day park hopped can be applied to the purchase of an annual pass. To get the most for your money, you'll want to use the ticket to enter a park first. Then visit guest relations, or a ticket window later, to upgrade the ticket. A few rules apply-- the ticket can only be upgraded in the first 14 days after first use, and might need to be upgraded before you have used all three days. (There seems to be some question about that last part.)