Disney doesn't always release all the rooms to the travel agents, so if there is a specific room that you want, you either need to call the travel agent or book online through Disney.
I always find it easier to book online, so if I am after a specific room and I can't find it through my travel agent's site, I will just book on Disney and then transfer the reservation to my travel agent. My agent gives me the same benefit regardless of whether I book initially through them or transfer later.
It may sound like a small thing, but if you are booking a B2B and want to have the same room for both cruises, you may only find the room available on Disney's site.