Building a controlor in Pixhawk using Simulink

Im using the embaded coder package for px4 autopilots to build a controlor in my Pixhawk.
I’ve followed the instructions gived in the manual of Matworks and all things works
The problem is that I have always one rotor wich don’t response to the set point.
The second problem is that I’m beginner , so i didn’t understand what every instruction to configure the Pixhawk to work with Matlab means.
Thank you for helping me.