Personally, I do not use any of the online travel sites.
I specifically use my airline website American or Southwest and directly book with the hotels, usually Hiltons or Marriotts.
I just booked a trip to SanDestin in August this way. Out of curiousity, I checked expedia.com to see if I could have done better and it was a wash. Actually, I came out better because by using the air, hotel and rental car sites, I keep the benefits of getting points and other deals available.
Good luck whatever you choose. I know everyone is different and has opinions on travel sites. We travel a lot and I do all of our booking this way. I will probably use some help next year because we are planning a tour of Italy and I need more detailed information so we don't miss anything.
Have fun!!