Although we are not driving the same shaft, our shooter design is a two-wheel shooter and we are using CAN and one jaguar's PID to control the speed of both wheels (motors) using the following method:
1) Set up the "speed" jaguar to speed mode and enable it.
2) Plug encoder into the "speed" jaguar.
3) Set up the other jaguar to be in voltage mode.
4) Set other jaguar to be set to the "opposite" (i.e. put a negative sign) of the output voltage of the "speed" jaguar
(-jag.getOutputVoltage()).
5) Complete the PID settings for that jaguar/motor.
Of course, I don't know how well this will work for you since your motors are connected to same shaft and you would have to use only one motor to set PID, but it definitely works for our shooter (still need to fine tune PID if possible--but that's another
thread).