KiCAD - Arduino shield - matching Arduino pins and schematic
A few minutes comparing some of the named signals will show that your two pictures pretty literally correspond; the only difference is that the two sides of the schematic version have been moved closer together to give more room outboard of them for names.
Simply hold your Arduino MEGA up to your monitor and you'll see the correspondence.
Then double check the actual PCB result against the labels on your physical board to make sure things ended up in the right places.