Do I target the AF of my camera on the "0" mark on the Ruler?

No. If you aim the camera to the 0 point on the ruler, 2 things will happen.

1 - The camera will no longer be "aligned" (parallel) to the focus target.

2 - The AF system could focus anywhere on the ruler. The actual focus sensor in the camera is larger and not necessarily aligned precisely as shown in the viewfinder. Thus we have the AF system focus on the focus target, and the "plane of focus" is in line with the 0 point of the ruler. This is one of the aspects of LensAlign that allows precision test measurement to be made.

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