The current version of the Manual GCP process is not intended for users that have geotagged images. it was designed to be used with cameras that don't have GPS information embedded in their tags.
The best way to process imagery using accurate GPS data is to use the normal geotag image based workflow and then use QGIS to accurately adjust the Maps Made Easy output to use your GCP data.
https://support.dronesmadeeasy.com/hc/en-us/articles/115003655066-Georeferencing-Aerial-Maps
The Maps Made Easy outputs are very accurate relative to themselves can be up to a few meters off of real world measurements due to the GPS accuracy of the aircraft.