The vertical move is the part of the alignment process that aligns the two shaft's centerlines into their proper up and down position. Usually you will have to add or remove shims in this step. The indicators are zeroed on the top and read at the bottom. (start with a plus + reading if you need to compensate for sag)
This means that the shafts are one half the total indicator reading from being collinear at these points.
Using a square grid graph paper to illustrate the position. Under the indicator position mark the point that is half the indicator reading. ( -6 for pump side indicator and +4 for the motor side indicator) Connect these two points with a line and then continue the line past the lines representing the feet on the motor. The graph now shows that the front foot needs to have a .003" shim added and the back foot needs to have a .001" shim added.
Now with your shims in place. Tighten all bolts and take and check your readings. If the readings are within tolerance than your equipment should be aligned.