Just the deposit. Once you qualify for the rate, it isn't taken away regardless of final payment method. It's more meant as a perk of having a Disney Visa. The percentage they take off the rack rate is typically the same as the discount released to the general public, but it gets released to Disney Visa Cardholders several days earlier, so it's the timing that is the perk, not the discount itself.
Something that provides an additional discount beyond what the general public sees (e.g. AP discount) requires that you show your AP at check-in (or have a valid AP assigned to your MDE account).
You'll be fine.
