I know it is an overasked question but I do not find anybody able to explain properly how to do that in SAGA 6.3.
The problem is that my shapefile, i.e. the borders of my country, do not overlap with the cities of the above country. I added the shapefile as a polygon and the cities as table then converted to points. Everything is plotted properly but there is a large vertical distance between cities and the country borders.
I had the same problem in QGIS and I solved it making the CSR consistent for the two layers. I am trying to the same here but with no success. Even if I change the CSR to EPSG 4326: WGS 84, they do not overlap.
What am I doing wrong?