I agree with the other posters! I booked a room with a great deal through Cheap Tickets (Owned by Expedia like Orbitz) since Disney had not released discounts yet. It took over a week of calling multiple times a day, being transferred, speaking with agents that had no idea what I was asking just to get my "Disney Confirmation Number" which is required to link the reservation to MDE. I also could not modify any room requests and had to check my bands were shipping to me rather than the agency. The Disney discounts released and I was able to book my same room and category for about $150 more. I ate the $25 cancellation fee and ended up paying the $175 more than I had originally thought. Totally worth it since I had the freedom to speak with Disney directly again. I will add that when I cancelled, I received my money immediately, but it took 3 weeks for the reservation to finally be removed from MDE! It was back and forth between Cheap Tickets and Disney. Cheap Tickets knew I cancelled it and refunded it, but Disney did not receive notification. Disney informed me that agencies do not update things right away, and it could take time. Cheap Tickets finally had to fax Disney reservations a cancellation notice and within 24 hours it dropped off and was all behind me.
How far away is your trip and will you be utilizing the Magical Express upon arrival? If it is relatively soon, I would say it may be too close to try and get it linked. I never tried booking the ME with this reservation, but I was unsure if that also had to somehow go through Cheap Tickets because it was not my reservation. There is the online form, but this also requires the Disney Confirmation Number.