Autonomous flight protocols?

DIY drone community,

What are the best practices and protocols for full autonomous, GPS waypoint control flight?

I'm moving away from manual and stabilized flight with my 450 kit build. My flight controller is a Pixhawk running a PX4 flight stack, using QGC.

I'm not entirely sure what the proper pre-launch and landing commands that bookend the waypoint flight commands. Plus the protocols; power, arm, flight mode... etc. are a bit unclear.

The pages is in flux (plus I'm running PX4) and their info on this matter is also unclear and most likly out dated. 

There must be standard well established protocols for this. I'm hoping that there are a few high-level DIYers out there who do autonomous flights all the time and that they have this figured out. Any help is appreciated or leads are appreciated.



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