We booked our 2005 FTW with Virgin and didn't really have too much difficulty to be honest. I have read on here that people do have trouble though.
I have mentioned on this forum in the past that you should really just think of Virgin as an agent for Disney, so they will book the date and deal with the first-stage paperwork, but most of the details can and should be passed direct to Disney.
We found at the time that the cost of the Intimate package was actually lower with Virgin rather than booking direct. We were fortunate that it didnt take long before our Event Manager contacted us directly. All the extras, add-ons and specific details were then dealt with directly by the fabulous Jennifer O'Leary at Disney (who is now Manager of the Cruise Weddings and absolutely fantastic).
We had the photo and video options available through Virgin, but made sure that they were excluded, instead opting to use Randy and Stan (STVS) - probably one of the best moves throughout the whole process.
So Virgin really didn't seem to do a great deal during the planning, but they were actually excellent when we arrived in Orlando. There was a rep to talk us through our plans at the airport and the actual Virgin Weddings planners based in Orlando phoned us at the hotel to arrange a meeting prior to the wedding. (we ironically poloitely declined as we were totally on top of our planss having spent a lot of time in contact with Jennifer).
So, the best advice I can offer is to book with Virgin if they offer a good price and then try to establish contact with your actual Event Manager. If there is no cost saving, go direct. At the end of the day, all the extras that you book (Carriage, Characters, Champagne etc) are all paid direct to Disney anyway. Just remember, Virgin Weddings are just agents for the FTW and probably do little more than just supply the information to Disney regarding the couple's plans....Disney will take care of the rest.