im trying to figure out how to connect
50:1 Metal Gearmotor 37Dx54L mm with 64 CPR Encoder to the Pololu Jrk 21v3 USB Motor Controller
where does the yellow and white go on the JRK? (AUX=A, FB=B ?)
what performance can i excpect with the amp limit of this cheaper JRK connected to the 12V/6amp motor?
Unfortunately, the Jrk does not support quadrature encoders.
The motor you linked to has a 5A stall current at 12V, so if you use it with the Jrk 21v3 and stall it at the full 12V for more than a fraction of a second, you will probably trigger thermal shutdown of the motor driver chip, and you could damage it. It will probably work, but to be safe, I would recommend using an acceleration limit and brake duration as well as not ever stalling the motor.
To expand on what Paul said, the jrk does not support using quadrature encoders for position control. However, if you are only interested in speed control, you can use one channel of the encoder as a tachometer; just connect either the yellow or the white wire to the FB pin.