It seem you are not familiar with Arduino neither do the FD. I am not familiar with Arduino too, just started. Same to FD04A.
Anyway looking at the product page of FD04A, I notice it has 4 channels of motor driver, so you can actually control 4 motor independently, need 4 PWMs for that.
OK, about arduino, as far as I know, it have at least 6 PWM pin, use analogwrite() function to output PWM signal, you can refer to arduino site for that,
analogWrite