The usual procedure is that you use the Arduino on the PCB as template for the holes and position, but when you actually make the PCB you solder a header on the PCB to plug it in.
In your case you will have to dummy fit it on the table or in your mind, and judge the male pin direction as to whether it will fit to the top or bottom side of the PCB. Just look at pin numbers and see if the FZ drawing is the same. If it goes on the other side press the bottom side button on the red bar at the bottom, and drag it in and it will be flipped looking at it from the top.