My first time out - I let the travel agent book all - boy have learned my lessons since then.
I go to carnival.com - look at a cruise - start clicking away and get price of cruise only and cruise + air.
When I get the air price - I go shopping for my air - I've always gotten the air cheaper. And also, I book a day ahead (just in case something goes wrong) and I book to return in the late afternoon I(plenty of time to get off the ship)
Hope this helps.