I see it the way, that the part stands on the PCB and somebody draw around its feets (or bottom part) to mark, how much place it take and that is the footprint. And manipulating the footprints to fit the place marks, where the parts should stand.
The footprint usually have both, where the foots(pins) touch the PCB and what place over PCB is blocked by the part.
Spend some time and learn. The Uno shield is already in the footprint library
So is the Mega
No need to reinvent the wheel
My usual response on that is always: “some wheels need grease to turn more smoothly” 
Thanks for the elaboration.
Did not know the MEGA is a bigger brother to the UNO.
It makes sense.
From the EAGLE PCB file:
Coordinates of D0... connector (center of 8 pins): (54.61, 50.8)
Center of A0 connector: (59.69, 2.54)
Center of ISP connector: (64.897, 27.94)
But yeah, this:
(When there is no pre-defined shield footprint, you can start with the published board/schematic design and delete all of the components except the connectors...)
