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Starting Ardu Pilot Mega
Here are the basics to check at the field:
Set your transmitter mode switch to "Manual". This is a safe mode in which to start up the system.
When you power on your board at the field, you should leave the plane motionless on the ground as level as possible (in flight position; so if you have a tail-dragger elevate the tail) until the three colored LEDs stop flashing (about 30 seconds). That means that the gyros have been calibrated and the plane is ready to fly (assuming you also already have GPS lock). If your plane is a tail-dragger, you should prop up the tail to level flying attitude during calibration.
After the ground start completes you should wait for GPS lock before flying. If you do not wait for GPS lock the home location will not be set correctly, and the barometric altimeter calibration will be incorrect. It should take less than two minutes to get lock. If you're using the !MediaTek module, the blue LED on the module will flash while it's waiting for lock, then turn solid once it has it. Once that happens, the red LED on APM should stop flashing and turn solid. If the blue !MediaTek LED turns solid but the red APM LED is still flashing, press the reset button on APM and once it reboots, the red LED should go solid.
BEFORE EVERY FLIGHT: Before you take off, hold your aircraft in your hands and switch to stabilize mode, then pitch and tilt the plane it to confirm that the control surfaces move the correct way to return it to level flight. This will ensure that you haven't accidentally knocked a DIP switch into the wrong position or otherwise reversed a channel. You should do this before every flight, just as you move your control surfaces with your RC transmitter to ensure that nothing's reversed. Failing to do this is the #1 cause of crashes.
It is highly recommended that you switch into either Stabilize or Fly By Wire mode and observe the behavior of the control surfaces. They should move to return the plane to level when you pitch or roll it. If it isn't rock solid, you can tune the gains by following the instructions here.
Unless you have tuned your configuration parameters for your airframe it IS NOT recommended that you take off in any mode other than Manual.
For your second flight, change the third mode (position 3 of your RC mode switch) to RTL in the Mission Planner's mode setup page.
This will test navigation. The aircraft should return to you and orbit overhead at a fixed altitude (which can be set with the Mission Planner).
Once all this has checked out, you can program waypoint missions and test then in Auto mode.