I was wondering the same thing. According to their FAQs
Q.
Can the Disney Gift Card for Honeymoons be used toward deposits for vacation packages purchased in advance?
A. If you booked a Walt Disney Travel Co. Magic Your Way Package or booked a room through Disney Destinations, once you have started to receive funds on your Disney Gift Card for Honeymoons you will need to contact Walt Disney Travel Co. (package) or the Disney Reservation Center (room only) at 407-W-Disney and change your form of payment to the Disney Gift Card for Honeymoons. You will then be issued a credit on your original form of payment.
Disney Vacation Club (DVC) Members who booked a reservation using their Vacation Points can instead use gift card funds to pay for their reservation. Note that changes to the reservation are subject to DVC booking policies and the standard 30-day change/cancellation policy regarding Vacation Points applies. Please contact a DVC representative at (800) ********.
Tip: To reduce the initial deposit expense when booking a stay at the Walt Disney World® Resort, only reserve room nights and use a personal credit card to pay the one-night deposit, then use the Disney Gift Card for Honeymoons to pay the balance with gifted funds.
I emailed them to clarify that, so I will post the answer when I get it!
Dear Samantha,
Thank you for your inquiry.
If you booked directly thru Walt Disney World, you can switch your
method of payment before you arrive. If you booked thru a Travel
Agent,
you will need to ask them to assit you with a change of payment.
As long as you or your
travel agent contacts our reservation office at
least 2 full days before your arrival, you will be able to switch your
method of payment.
Please contact us if you have additional questions at 407-566-7272,
Monday - Friday, 9am to 5pm or use this email address.
Best Wishes,
Rochelle
Disney Honeymoon Registry Team