if you put the shim under the work piece and place the machine on the same surface as the shim the reference face becomes the surface that touches the shim. if you put the shim under the domino fence and on top of the workpiece it makes the reference face the opposite side. is that clear? it's hard to type this out.
basically this, it changes which side of the plywood will be exactly flush. if you want it to be the inside of a box then place the shim under that way the inside of the box aligns perfectly. if you want the outside to align perfectly place the shim on top and use the fence on the tool.