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http://ardupilot-mega.googlecode.com/svn/ArduPilotMegaImages/missionplannerfirmware.PNG
Starting with APM 2.0, the easiest way to load the APM firmware is to download the Mission Planner, which will load the code for you.
You can download the latest APM Mission Planner here (it will be called APM Mission Planner(xxx).zip). Unzip it to a folder on your desktop and run !ArdupilotMegaPlanner.exe.
It requires a Windows machine running .net Framework 3.5+. 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. If you're using Windows XP you will have to download it yourself here).
When you plug APM the first time to your PC and are running Windows 7, it should recognize the FTDI USB-to-serial chip and install the right drivers. But if it doesn't or if you're using an earlier version of Windows, you should download and install the appropriate driver for your Operating System from here. Once you've done so, reboot your PC and plug in the cable again.
(Note: Make sure you're using a regular USB 2.0 port and not the new USB 3.0 (!SuperSpeed, or "ss") ports. APM is not currently compatible with USB 3.0.)
APM should now be recognized and show up in your Windows Device Manger (which you can find in the Windows Control Panel) as shown below (your COM port will probably be a different number; it's assigned by Windows based on how many other devices you've connected). That's the COM port you'll use in all USB interactions with APM. It's a good idea to right-click and select Properties, and ensure that the "Set RTS on close" box is checked, as shown.
(Note that if you're also using an Xbee wireless module on this computer for in-flight telemetry and mission planning, Windows will assign that module a different port, which you can also see from the Control Panel.)
http://ardupilot.googlecode.com/svn/images/eighteen.jpg
If your APM is plugged in, the COM port it's assigned to should show up in the Mission Planner. Ensure that the baud rate is set to 115200.
Do not click "Connect" yet! You must load the correct firmware for your vehicle first.
To do so, select an icon in the the screen below. Select the blue aircraft if you want to load code to fly your plane; select the green aircraft ("Xplane Simulator") if just want to connect your board to the Xplane Flight Simulator. The Mission Planner will autodetect what kind of board you have, download the latest code from the Internet and load it on your APM board.
http://ardupilot-mega.googlecode.com/svn/ArduPilotMegaImages/missionplannerfirmware.PNG
(Note: If you want to program APM using Arduino, you still can. Instructions are here)