https://support.dronesmadeeasy.com/hc/en-us/articles/360000518146-Manual-Rereferencing
Our manual GCP referencing process is done after the initial processing.
The GCPs are surveyed coordinate locations. If you just want the map to line up with the basemap better you could pull the coordinates for the GCP locations from the basemap by right clicking on the map in the Map Detail page.