Reading the information at http://www.robotshop.com/content/PDF/Overview-1212.pdf, I would connect IN1 and IN2 to Arduino output pins, and D2 to a PWM output pin. Connect D1 and INV to ground. Connect EN to +5V unless you want to be able to power the motor driver down, in which case connect it to another Arduino output pin.
In this configuration, you can select forward (with PWM), reverse (with PWM), braking and coast modes.