The Disney site is definitely a tool, but as a former travel agent, I also used Southwest air vacations and Funjet vacations for all inclusive Disney. I found Funjet and SWair to be cheaper often - you just have to check. Both offer Disney and nonDisney hotels . I do think it's easier to stay in a Disney hotel, b/c, for ex. whatever you buy in the parks will be delivered to your hotel.
Whenever I travel, I check out the hotels on Tripadvisor.com to see what people have said about them and to see vacationer's pics. They will give you a lot of info in addition to the rooms/hotels. Great tool!
I would do my research, find out exactly where I want to stay, what I want included, etc, go to Funjet, SW, Disney, or even Expedia, Yahoo travel, etc (I've had Funjet match prices I got on these other companies) and once you've got everything you want, including price, call a travel agent and have them book it - exactly what you found, price, etc and they should be able to get the exact same thing. You can't wait a day, though - prices change all of the time. You have to call when you find what you want. It's just nice to have a local person to go to w/questions, etc and the price will be the same.
Also, it's a good idea to get the insurance in case you have to cancel.
FYI, apparently they are going to build a Disney in Bastrop, Texas in about 7 years.
I hope that helps. Take care,