We recommend that you use the Mission Planner for first-time APM setup. (It's designed for Windows but will run in a Windows VM on a Mac or under Mono under Linux. Or, if you don't want to use either of those, you can use the CLI mode, which will work on any operating system.)
After you've downloaded the firmware, ensure that you've got the right COM port and baud rate (115k) selected, and click on Connect in the top right corner. The Mission Planner will now connect via MAVLink.
Now you can click on the setup button circled in red below:
This will open up a dialog box that will walk you through the basic setup process, described below.
Note: you MUST have an ESC or other 5v source plugged into your APM RC pins to power your RC receiver. USB power does not power the RC receiver. If you do not separately power the RC system, APM will be unable to read any signals on its RC inputs.
1) Calibrate your RC input
You must be powering the APM RC pins (with an ESC or equivalent 5v source), and your transmitter must be on. Ideally, you have already flown your airplane in manual RC mode and adjusted any trim values necessary, so the RC outputs reflect these trim settings; if you haven't already flown your aircraft in RC mode and trimmed it out, you may need to do the RC calibration again later, after you have flown the aircraft (this is easy to do at the field).
Channel assignments are as shown above. When you move the RC sticks, the relevant bars will move. Click on "Calibrate Radio" to set the radio limits. Red bars will appear, and you should move them to their limits for each channel you have connected.
On this screen you can also reverse servos if necessary and set up elevon mode if desired.
Press "Click when done" when you're done.
2) Set your flight modes
You can choose different flight modes in the air with your RC transmitter's toggle switch, which you should have connected to APM input 8. Full details on the available modes are here. (If you want to get more than three modes from your transmitter, a guide is here) When you move the toggle switch, you will see the green highlight change to a different line. You can use the drop-down menu on each line to assign that mode to a function. Note that Flight Mode 6 cannot be changed from Manual. It's "hardware manual", which means that it's controlled by the failsafe circuit on the APM board to always be able to return you to RC control as a safety measure.
3) Configure your hardware
In this tab, you can tell APM what optional sensors you have connected. Just click the check box for any sensor you're using. (Sonar is not currently supported with APM; it's primarily used for ArduCopter)
For the magnetometer (compass), you have a choice of calibration options once you enable the sensor:
To manually enter a declination for your geographic location, you can find the correct value by clicking on the link to open a web browser. Enter your location and it will give you a declination, as circled below:
In this case, I would enter "14.13" into the magnetometer line (the software converts from decimal to degrees/minutes).
4) If you're using a standard airframe, load a pre-made configuration file
For common airframes such as the Bixler, Skyfun and Skywalker, we have supplied configuration files which are tuned for those aircraft. You can download theme here and use the Mission Planner to write them to APM.
5) Now if you switch to the Flight Data tab with MAVLink connected, you will see the artificial horizon moving with the board. Remember to leave the board stationary for 15-20 seconds when you switch into this tab, since the IMU must calibrate first. Once it's done, the HUD will start moving.