I've done it both ways. Prefer the travel agent. The agent is a friend and so she goes out of her way to find everything she can for us. My wifes cousin on the other hand prefer to do it themselves. They do a lot of research and so find a lot of good deals. In the end we are pretty close price wise, but I don't have to do much work
Do it ourselves. We drive so flights are a non-issue for us. Half the fun for us is researching where we want to stay and places to eat each day. We use the Disney World site and Birmbaum's books as well as Disney forums like this and a few others.