The movement paramaters are setup in the intial configuration in the ini file. You access this from the "Configure" menu. After you tell it the number of axis, you then tell each axis the amount of movement per step in the "Scale" parameter. This number will be based on the encoder count, drive reduction (if the encoder is mounted on the servo or stepper is not direct drive), and pitch of the screw.
It is pretty well documented in the manual. Give it a read and if you have problems, get back to us.