Using a microcontroller for something like that would be a difficult task. It might be feasible to create your own computer software to read the values from the potentiometer and then set the jrk’s PID parameters over USB. A good starting point towards accomplishing that can be found in the “Writing PC Software to Control the Jrk” section of the Pololu Jrk USB Motor Controller User’s Guide.
The Arduino can control the jrk through its serial interface using a library like SoftwareSerial. More information about the jrk’s serial interface can be found in the “Using the Serial Interface” section of the Pololu Jrk USB Motor Controller User’s Guide.