PM Modes - arthurbenemann/ardupilot GitHub Wiki

You can set your RC system up so that you can choose between either three modes or six modes using the mode selection channel. (The available modes are described here.) Selecting between three modes is easily accomplished if your transmitter has a three position switch. You must setup your flight modes using the Mission Planner or the CLI before first flight or all your modes will be set to Manual. It's also possible to get six modes from most major RC transmitters; this page gives instructions on how.

Move the APM slider switch to CLI mode and open a terminal program. Once in the CLI, select Setup and then Modes. Move your RC toggle switch to the position you want to assign, then move your aileron stick right or left to increment between the various modes available. Then do the same for the other toggle switch positions. When you are done, press the Enter key to save and exit.

Here's an example:

http://ardupilot-mega.googlecode.com/svn/ArduPilotMegaImages/modes.png