Due to manufacturing tolerances, the leadscrew and the carriage nut on the StackShot rail do not fit together perfectly. As a result, when the screw reverses direction, it must turn a small distance before the carriage actually moves. This slack or lost motion, called “backlash”, typically corresponds to about 0.1 to 0.2 mm of carriage movement. The StackShot controller knows how to correct for backlash, but because it cannot directly observe the carriage movement, you have to tell it what amount of backlash your particular rail has.
There are two good ways to set the backlash value. Both of them start by putting on your highest magnification, thinnest DOF optics, mounting up a subject that has clear detail, and observing focus either through the viewfinder or via LiveView.
Method A is generally more accurate and corresponds directly to having the fine focus knob work well. However, method B should get you a good starting value pretty quickly, and going through both processes will help develop a good intuition for what's going on with the hardware.