Microstepping is accomplished by driving a sinusoidal current waveform to the stepper motor windings.
Assuming you are using two stepper motors (one for each wheel), you would need 4 channels (2 per motor) of PWM outputs if you intend to control the phase currents of the two motors. If the microcontroller has A/D inputs, you can utilize them after some amplification to sense the magnitude of the phase currents and have full closed loop control of the currents.
I'm not familiar with your microcontroller, but it takes a lot of the controller's computing power to regulate the current even for just one motor. An easy solution is to use a dedicated microstep driver for each motor to off-load this task.