The only way (that I know of) is to do it through the DCL website.
That is after you book your date and category, you will see on the left hand side under the "Air Travel" it says "Resorts and Tickets" you can click on that tab and it will allow you to book WDW packages (room/tickets, etc).
I don't think you can do it the other way (booking through the WDW website), but I am not sure!
You can also have a TA look up prices and dates for you or you could call disney directly. Their transportation will take you to and from the resorts, but you do pay extra for that.