3D Compare is a great tool to get a simple visualization of the deviations between the reference and measured data. If desired, it can be contained to specific reference faces. 2D Compare works in a similar way, but is constrained to a 2D section. This section can be customized to zigzag through multiple cutting planes.
The 3D/2D Compare tools have the ability to create tags. This is useful for calling out max/min deviations. For any other method of tagging, it is better to create them with the Comparison Point tool as explained in this article.
This graphic is useful for understanding the settings for the comparison point:
Note: The compare results will not be affected by changes in the Pairing Manager.