booking online through a site such as expedia is a good way to often get a good rate, combined with options. but the issue at hand is that you will have to be your own travel agent, just as if you had booked directly with the airline. you need to check flights and times with the airline schedules to be sure that there is enough time between connections to get to your next flight, and check your reservations ahead of time. these companies make money in volume sales, and like anything else, you get what you pay for.
fyi, on the west coast most often southwest airlines has better deals if you book enough ahead of time than you can find on any package/cheap rate sites.