First, one should align the lithophane vertically as that way you have better resolution than printing flat against the bed.
Secondly, they need to be aligned with long end in line with the direction the bed moves. For an Ender 3 using Cura as a slicer, this would be the y-axis.
The reason for aligning them with the bed's direction of travel is because since they are tall and thin the lithophane would be more likely to fall over or vibrate otherwise.
In Cura, it should look like this,