running a dc motor with a small L298N module and an arduino and the L298N library
PWM is used to control the duty cycle and not the voltage directly so your PWM will work directly on the input pins of motor driver and you will be able to control the speed.
just use analogWrite on the input pin which was held HIGH and HOLD the other pin to LOW. If you desire to change the direction while simultaneously controlling the speed. just analogWrite both the pins. Just keep in mind that the duty cycle of both the pins should not be tweaked simultaneously. while the speed is being controlled in one direction the other pin should be at analogWrite(other,0).