The Mission Planner, created by Michael Oborne, does a lot more than its name. Here are some of the features:
Note: You can also do mission planning with the HappyKillmore GCS, which also has point-and-click waypoint entry and full scripting. It's really a matter of personal preference which you decide to use. The HK GCS instructions can be found here. The rest of this tutorial will focus on the APM Mission Planner.
Download the Mission Planner here (it will called APM MissionPlanner(xxx).zip). It requires a Windows machine running .net Framework 2.0+ (this is shipped as part of Windows Vista and Windows 7, so if you're using them you don't need to load anything more).
The Mission Planner will open a task bar at the top of your screen, and open with the Planner window. In the Options menu on the task bar, select the Com port assigned to your APM board.
NOTE: The Mission Planner supports both APM and ArduCopter. Make sure you choose the functions from the menu that correspond to the software that you're using!
The main Mission Planner function is represented by a tab in the top row of every screen. Each is described in the menu items in the left column of this manual.