I have not purchased yet, but I would think that if you log into your Disney account before trying to buy the tickets, the passholder rate would apply -- assuming that you have already been to Disney World and gone to Guest Services or a ticket window to activate your Annual Pass.
If you purchased your Annual Pass but have not gone to Disney World yet to activate it, then it's possible that the passholder discounted rate would not show on the website and you would have to call to get the discount. I'm just guessing about this, based on what happens for some people if they purchase an Annual Pass, have not activated it yet, and try to book a hotel room with the passholder discount.
Mainly I'm just trying to bump up your question (of how you get the Passholder rate applied to your tickets).