It has been our experience that airlines' websites have better fares than Expedia, Orbitz, etc. (the fare is the same, but no $5 add-on "processing fee" or whatever it is) - but I can see that if you are going on multiple carriers, these sites may provide a cheaper fare. What I have done in the past is call the airline who carries you from your point of departure and mention the fare you found on one of those travel sites - they should match it. Then, your upgrade should come much more easily. Best of luck!