I'm still using Bencox software, so can't comment on others, but what I did was placed a piece of balsa in top left corner, and cut it with the laser, using a rectangle. This has become my jig for quickly finding the zero point in x/y
Then I when I make a drawing, i usually make it on a background equal to A5 size, 148x210mm, and dpi=254DPI, or 100pixels/cm.
Then when I import the drawing, its in the right place and correctly scaled. Makes getting the right spot easy each time.
In inkscape i often place a circle of the size of the item I'm about to cut, and then move the circle out of viewing area just before exporting it as a png.
Your magnets look great.