Easy way to do coins flawlessly:
Design both sides in a single file. Use a different color for each side, have them overlapped and oriented in the direction you want them relative to one another.
In addition to having your engraves both in place and different colors, you will have your circle for cutting the coin AND a square which encloses that circle. Circle and square need to be different colors than one another.
Hold down your work piece with magnets or some other means to ensure it will not move later.
Engrave side 1, and cut the SQUARE. Ignore side 2 and circle.
Flip over every square. Be sure not to move the main board during this process (use razor blade to lever squares out via kerf).
Engrave side 2, and cut the circle. Ignore side 1 and square.
Coins done.
Flipping every square on a sheet with hundreds of coins is a pain. But for me personally, less of a pain than trying to set up the file so I can flip the entire workboard and have it stay in the right place.
You can do larger squares (5x5 coins in a single square) to save some time for large orders.