Full Disclosure- I am just a mom, my advice and knowledge comes from my experiences only. I have never booked any of my trips through a travel agent and I have held Annual Passes for the past 8 years and only been to Orlando. Please keep this in mind when I am giving advice. I have a teenage son with Severe Autism so many times my comments might reflect our experiences with dealing with that in the Parks.
The best place to start is to open a My Disney Experience account. When you first Google Disney you will come across different web addresses.
www.Disney.com - Everything Disney and links to everything Disney.
www.ShopDisney.com- Anything you want to buy is here. I love the clearance section!
www.DisneyParks.disney.go.com All Disney vacations including cruises.
www.Disneyworld.disney.go.com Specific to Walt Disney World vacations. Here is where you want to start when planning a trip to Walt Disney World, Orlando. In the upper right hand corner you will see My Disney Experience link. Click on it and create an account. Once this is done they do a good job of walking you through it. When you call WDW reservations at 1-407-934-7639 the agents are inputting the information you are giving them into the same system that you see here online. If you are a Florida Resident and/or Annual Passholder make sure to check the deals for these rooms. If there are any deals they will display above the room you have chosen.