Often the AP discount applies only to a certain number of rooms or a certain room type (for example, only the pirate rooms are available right now for the dates I've looked at in May - and I've been looking at dates in the entire month of May. While you might be able to convert a room that's already booked there's no guarantee they'll have the same room category available so you may have to cancel the initial booking and rebook at the AP rate. They haven't yet announced the AP rates for September, and keep in mind, if you do the AP discount you can't get free dining as well. Depending on the number of people you're traveling with you'll have to look at the numbers to see if the discount or free dining is the better option. The AP discount is typically about 5% more than the discount that they offer to the general public (which often are 20% or 30% off rack rates, so the AP is 25% or 35% off the rack rate). Although I just looked at the room I have booked at CBR, and the dates I'm going. For a Standard Pirate Room the rack rate is $265. The current room only discount that anyone can get (Fun and Sun offer) is a rate of $225.25 or a 15% discount. My AP rate is $185.50 which is a 30% discount.
When I do online check-in I've never had anyone verify that I have an AP. When I've checked in at the front desk I've also not had anyone ask me to verify my AP, but I also usually have it out with my ID and CC, but that might vary by cast member. I know that I cannot see the rates for AP holders online unless I'm logged into my account and can only reserve them at that point as well (when the system is working, it's currently having some glitches that won't allow me to book a room online). I believe you might be able to reserve a room at the AP rate if you call to make the reservation without having the AP. I know that if you've already purchased the voucher for the AP you can make the reservation with the AP discount.