I'm a consultant and book all of my own travel.

If you're tied to using the travel desk of the company you're consulting for, then you need to give them the flight numbers of the flights that you want to take. As the previous poster says, stick to the same airline alliance.

If you do some research on fares in advance, you should be able to give them flights that are reasonable value compared to the cheapest available. This way they will have little argument about booking the flights you want, rather than the cheapest ones available.