An example, this is how I deal with my Beseler (after first adjusting each blade to be perfectly square with the appropriate screws):

Side to side: Even though a new sticker is available, I found the paper aligned perfectly with the right side of the channel, so I just use that.
Up and down: I determined the scale is off by 1/8 of an inch. So, after setting my margin, I go back and move the top blade down 1/8" and move the bottom blade down 1/8"
It is easy to determine if the scale is correct; put a sheet of paper in the slot, then bring the bottom blade even to the bottom of the paper. The scale should read exactly the paper size. Bring each side blade in to the edges of the paper and, again, the scale should correspond to the exact paper size.