Hi, Christie,
Regarding your question, as you know in bipolar mode, the PWM signal pair is in complementary mode, in other words, the PWM2n and PWM2n+1 signals are invert for each other, this is the table for the voltage impressed on the motor branch:
for example, the PWM0/1 are connected to PhaseA, PWM2/3 are connected to PhaseB
PWM0/1 are set as 0% duty cycle, the PWM2/3 are set to 0% duty cucle, and PWM2/3 pair is inverted, in the case, PHaseB is +VBus, PhaseA is -Vbus, the motor gets maximum power.
PWM0/1 are set as 50% duty cycle, the PWM2/3 are set to 50% duty cycle, and PWM2/3 pair is inverted, in the case, PHaseB is +0V, PhaseA is -0V, the motor gets no power.
PWM0/1 are set as 100% duty cycle, the PWM2/3 are set to 100% duty cycle, and PWM2/3 pair is inverted, in the case, PHaseB is -Vbus, PhaseA is +Vbus, the motor gets maximum power.
I do not suggest you set the PWM duty cycle manually, we have the BLDC code, in the code, the velocity loop set up the PWM cycle with PID control.
Hope it can help you
BR
Xiangjun Rong