Just use them as an airforce... or instead of horses
Its also a good idea to use them in the manner in which Christopher Paolini describes in his books.
Uhm.. Isn't THAT how he uses them? blah-di-blah-blah-blah link with the rider and all, but in the end, there are dragon riders..
(didn't read the last one yet, since I'm yet to find the proper sized paperback - he's no Martin, where I got the first BRICK edition of Dance I found, and will buy the proper paperback when I cross it)