Hello Shery,
I do not understand what you mean by "multiply the output of the PID PWM generator with the inverter commutation signals" in the context of my understanding BLDC motor control. Did you do any basic simulation on BLDC control before modifying the Simulink algorithm? The conversation on the control algorithm is one maybe you should be having with Boston Engineering or Mathworks.
I am sorry that I am not able to help you here.
Regards,
Aengus
