Actually, the advice in that video isn't the best given. As mentioned in the comments of the video itself. You should set the snap to .5 the original tile size, and use snapping.
So for a 128x64 tilemap, you would set it to 64x32. This sets the snapping on exactly the right coordinates, and you can't misclick it like you would be able to with a 1pixel snap.
Hope that helps :)