I use ORBITZ as a Fare Finder, and then book the travel on the airline's own website.
For example, I did a recent search and found a NYC-LON R/T economy class flight during July at an unbelievable $520 on AA!
I went to book it on AA and it was 540 there, however, I was willing to accept the $ hit, as I had never booked on AA.com before, and I knew there was a 5,000 mile booking bonuse for 1st timers. Little did I know that there was another 5,000 mile booking bonus for first timers. I signed up for both and we will see if I get boths, as I have e-mail confirms to that effect.
Anyway, I do not know if the $520 Orbitz flights would have been "converted" to the more costly $540 flights that I finally booked on AA.com, but if the costs are nearly the same, it might be worth it to use Orbitz as I have done, and then book on the airline's own on-line website for their extra mileage booking bonuses!