Put a small hole near 3 corners of your design. If they can be ‘far’ away from any of your vias or through-holes, they are very easily recognized. I use 0.7mm holes because everything I do always has 0.7mm holes anyway.
Do not put them extremely close to the ‘top’ and ‘bottom’ edge of the board, or you might be trying to drill through the board clamps.
Because when you go to align the second side of the board, if you have placed the board wrong, you will not be able to align to all three. If the board is placed in the correct orientation, you can select each of the 3 fiducials for your alignment.