It sounds like your wiring might be correct. You can also power the encoder board through the blue wire by connecting it to one of the 5V output pins on the jrk (if you are not already powering it from a separate 5V source).
When using frequency feedback, you will probably want to adjust your feedback scaling in the "Feedback" tab of the Jrk Configuration Utility. To calculate what the "Maximum" should be, it helps to understand how the frequency feedback works. The feedback is reported as
2048 + n (where
n is the number of pulses measured in a single PID cycle). Note that since the feedback value must be between 0 and 4095, the jrk can measure a maximum of 2047 pulses in a single PID period; you can modify the PID period in the "PID" tab of the Jrk Configuration Utility. You should be able to determine the maximum pulses you expect to receive from your encoder since you know the approximate RPM of the motor and the PID period.
Once you have your feedback scaling set, you can check it by using the pull-out plot of variables vs time, and making sure the "Scaled feedback" variable changes from 50% when the motor is stopped to 100% when the motor is going full speed in one direction and down to 0% when it is going full speed in the opposite direction.
I am not sure of what PID coefficients might work well with that particular motor, when using frequency feedback with the jrk the integral term is particularly important. It might take some trial and error to get the PID coefficients tuned well. You can use the same plot of variables vs time to graph the error, or compare the scaled feedback to the target, while you are adjusting the terms.
There is some additional information (such as an example of calculating the maximum pulses per PID period) that you might find helpful in this thread. The original question in that post is about controlling the motor speed in a single direction, but a lot of the explanations still apply to your case.