That instruction guide should help. The pictures are pretty clear.
If you measure the shims above the lip and measure the inside length of the stem opening, you’ll see that the shim sits about 3mm below the top edge of the stem when inserted. That gap should be constant no matter which shim is used or whether it is used as a negative or positive shim. The steerer tube should come to the top of the shim, which gives a gap of 3mm to the top of the stem.
However, depending on the head tube angle of your bike, washers or shims installed below the stem, and how the steerer tube was originally cut, it may or may not be quite flush with the top of the multi position stem shim. Keep in mind that this stem is an after market option on your bike. So, if the steerer tube is a little high you should still be able to use this stem as long as the top preload cap fits onto the stem correctly.
Be be sure to follow all of the precautions and warning in the guide. Expander plug position and torque setting are very important, especially if the steerer tube is carbon.
If you you have any doubts about the fit, you should really check with a reliable local bike mechanic.
Best of luck!