Ground Control Points (GCPs) are used to georeference the model. A minimum number of three GCPs is needed to scale, rotate and locate the model, but it is recommended to have between 5-10 GCPs, well distributed over the area, depending on the terrain, the difficulty of the area and the height differences. If there are abundant GCPs in a project, some of them can be used as checkpoints to assess the accuracy of the project. GCPs improve the relative and the absolute accuracy of the model.
For more information about GCPs: https://support.pix4d.com/hc/en-us/articles/202557489.
Checkpoints are used to assess the absolute accuracy of the model. The marks of the checkpoints are used to estimate its 3D position as well as potential errors in the clicks. This way, the relative accuracy of the area of the checkpoints may improve. The difference between the initial and the computed positions of the checkpoints is displayed in the quality report and it gives an estimation of the absolute accuracy of the model in the region. For more information about the Quality Control of a project: https://support.pix4d.com/hc/en-us/articles/205148245.