I typically just go with wherever I get the best rate. Sometimes that is through Disney, sometimes that is through a site like Orbitz. From what I can tell, there is no drawback to booking with an outside site. For example, a week ago we decided last minute to travel down in three weeks. There weren't any great rates left through the Disney site, but Orbitz had some good rates. On top of that, they have a 15% off code right now. I got a substantially better deal on the same room I was considering booking through Disney.
Once I made the reservation I called Disney, asked them to look up my reservation, and asked them for my 12 digit, Disney-specific code. I then linked the Orbitz room to My Disney Experience, and it shows up just like if I had booked through Disney. I was able to do online check in, link it to my tickets and FP+. I encourage anyone interested to give it a try, it really could not be easier!