What PWM frequency? Are you going to drive the motor with simple square wave? Or pseudo sine wave?

If it's simple square wave drive, that's easy, just start PWM1, wait the time that corresponds to the phase required, start PWM2.

If it's pesudo sine wave, then update two different pwm timers in their own interrupts.

I understand that the phase shift is fixed. So you only have to make the 360º sine wave.

Make a table with pwm values, and a "phase" variable.

PWM1 interrupts takes next PWM value and updates the phase.

PWM2 interrupts reads the phase and sets the PWM value adding the wanted shift.

I know the pictures are 3-phase but it's the same.