Another Missourian here. In answer to your question I found that booking with a TA was best/cheaper. I tried pricing it all ways, through disney, alacarte, expedia, funjet etc. And I called the TA who had booked my first trip to WDW in 03 and she came back with a quote that was almost 500 cheaper than any other way I had tried.
I have always found that booking on my own has been the best way to go. I use the search engines like Travelocity, Expedia to get an idea of the airfare for my area. I then go to the airlines websites and check for better deals and I book my own airfare.
This way you have your choice of airlines,and the times that you want, for the price you want.