Hi Sylvain,
In general, you can't really calculate the PID gains in the autopilots, since you don't really know the system and it is a bit difficult to characterize using simple traditional methods (i.e. without getting into serious system identification). So, you have to start with some of the example coefficients in the example airframes, and then tune in-flight empirically by observation. Looking at the logs/live plots helps too. It certainly helps to understand how the control loops work when tuning.
Thanks,
-Stephen Dwyer