Because you are testing a manual lens, we can break some rules that are only applicable to AF systems.
Working backward, there is actually no reason NOT to focus on the "0" line of the ruler. With an AF system we cannot do that because we would have no way to assure that the AF system would actually focus on the "0", and not the "1" or "2" or whatever. However, when testing a manual lens you are actually testing the camera's manual focus system as well as the photographers eye/hand coordination and capability. In this case we have some human intervention that is capable of knowing that it is the "0" that is our target.
We would recommend that you use the right hand sighting hole (closest to the Ruler) and align the camera with that and then test the focus by manually focusing on the "0" line.
All of the above is applicable only if the camera/LensAlign distance is rather small where the "0" line is a sufficiently large enough target for your eyes to manage.