Back EMF protection on bidirectional DC motor controller
I am unsure of where to handle the back EMF in this circuit


If you read the data sheet and look at the diagram on page 5, you’ll see that the chip uses a H-bridge of 4 MOSFETs. Those MOSFETs contain bulk diodes that pass back emf from the motor to the power rail: -

 

My words are in red.

So, all that you have to ensure is that you have enough bulk capacitance on the 6 volts (from the 7806 regulator) to avoid that voltage rising too high when the motors are free wheeling or producing back emf.

If potentially problematic, add a zener diode across the 6 volt power rail.