IMO PWM_SMMR (or TC_SMMR) is the register to be used for H-bridge control. You will find PWM waveforms outputs to provide a 2-bit gray count waveform on 2 outputs page 981 of Sam3x datasheet. Unfortunately, Figure 38-6 is wrong but you can find the correct figure (Figure 39_6) page 962 of Sam4S datasheet.
Whenever you have to code PWM waveforms, it's handy to draw the waveforms you need for a few periods, then look for the proper registers to program.