More info on the clone tool here: https://docs.gimp.org/en/gimp-tool-clone.html
Clone takes some part of your map (the source) and clones it to somewhere else. As Xorne was doing in the video - he selects a blank portion of the map as the source and then clones this over the section of the map he wants to overwrite with data from the source.
If you set the source as the apex of a grid where there are no GM markings (CTRL+Left Click exactly on the apex with the mouse cursor - you will see cross-hairs appear at the exact point you selected) and then start cloning exactly on an apex where you wish to overwrite with the source (position the mouse cursor exactly on the apex and left-click-and-hold) then move your mouse (still holding the left mouse button down) to cover the extents of the area you wish to overwrite.