If you add a code to an existing reservation, they just adjust your balance of how much you have left to pay at check-in. If you book straight out with an AP, you have to just pay one night's deposit and the rest upon checking in.
You can book via phone without an AP, as they do not ask for your AP number, just that you have it with you upon checking in. When calling, tell them you have an existing reservation and would like to apply the said AP discount. Your particular resort may not be offered, but they more than likely will give you alternatives if you are open to move.
In order to book online, you must have an AP number in hand to enter the site.
Remember, in order to check in at your resort with an AP rate, you have to have a valid AP, not a voucher, to show the CM. So, if you order an AP voucher in advance, you have to go to Guest Services at one of the parks or DTD to activate it before checking in.