How to tune PID Control Gains?

[dssdyx]

This project is an amazing work. And I also try to learn and run it on real UAV.
But I have some confused about tuning SO3 PID gains. There are 3 gains: position gains, velocity gains and position error integral gains.Which gains should be first tuned and how to do this step?
I have a little experience of using Pixhawk 4. I know if I want stable flight controlled by position setpoint, I should tune attitude loop firstly and then tune velocity loop and finally tune position loop. In so3 controller, is it the same step to tune these gains? Would you like to tell me tricks about it? Thank you !