C.A.
You can go straight through Disney by calling them or by using their website. They are the most experienced with their own company. If you do decide to go through a travel agent, I would also call Disney direct anyway and see who can give you a better deal. In addition, there are many websites that seem to give you discount prices and they may be worth exploring. Whoever you work with, make sure that they really know DisneyWorld. It is very large and imposing if this is your first time.
No matter what you decide to do, get familiar with all of the hotels and their placement on the property. Each hotel is very different and their locations will determine how long it takes to get to certain parks. For instance, Disney Wilderness Lodge is located near the Magic Kingdom by a quick boat ride. You need to take a bus to get to the Animal Kingdom and the other parks and the bus rides vary in length. However, Disney's Wild Animal Lodge is closer to the Animal Kingdom but you will need to take a bus to each of the parks if you stay there.
By familiaring yourself with the overall layout and the different hotels and their adjacent parks, you will feel more comfortable when you are there.
Enjoy!