I would just book the staterooms, either with the cruise line, or a travel agent. Then do your research on the airfare. All of my previous cruises, my stateroom and airfare were booked separately, as the airfare was cheaper through the airline directly and not through the cruise line.
2007 - Majesty of the Seas (Bahamas)
2009 - Enchantment of the Seas (Western Caribbean)
2010 - Freedom of the Seas (Western Caribbean)
2013 - Golden Princess (Alaska, roundtrip from Seattle)