Three phase pulse width modulation (PWM) consists of three signals modulated by a sine wave. The duty cycle or high time is proportional to the amplitude of the sine wave. The effective average voltage over one cycle is the duty cycle times the peak to peak voltage. Thus, the average voltage follows a sine wave. In fact, this method depends on the motor inductance to integrate out the PWM frequency. These waveforms in the graphic to the left are aligned by the leading edge. Thus, the top switches all turn on at the same time. This movie is ideally what you should see on the oscilloscope. The frequency is very low and the modulation depth is 100% to permit easy viewing.
A better method is to align the centers of the three wave forms. The motor will actually respond to the difference between two phases. By aligning the centers of the three PWM waveforms, the three motor windings are switched more often. This reduces the level of harmonics, reducing audible noise. This method also can provide twice the resolution for the same switching frequency. However, the digital timer is more complex. The MC9S08MP16 was designed to support center aligned PWM.