Hey,
I would first try this:
Use 3-PWM mode on the PHASE inputs, and use the BRAKE input as the enable signal. Or you could try the other way round, using 3-PWM on BRAKE and PHASE on enable.
The BLDCDriver3PWM has a constructor that takes 3 pwm and 3 enable pins.
May I ask why do this, and not just use a “more normal” BLDC or half-bridge driver?