[gpetilli]

Since you mention CAN, I assume you are using the PID on the Jaguar.
For position control, we prefer the potentiometer over an encoder mainly since it maintains the home position through power cycles. Depending on your application, the encoder will likely need a limit switch and a power up calibration to find home. We have been successful using a pot tied to the Jaguar running PID in the past - however if the load is asymmetric (think arm working against gravity going up vs. with gravity going down) it is difficult to stabilize with the textbook PID in the Jaguar.