Registration marks, as in the traditional target variety and all of its variations, are a waste of time.
If you want to register multiple layers of vinyl cut a rectangle that bounds all of the layers on the base vinyl. That would be the one you apply first. Then cut that same rectangle, or weed border if you prefer that terminology, exactly the same size as the rectangle you put on the first layer.
Mask all the layers and trim them about 1/4" to 1/2" larger than the bounding rectangle.
Apply the first layer including the 1/4" to 1/2" of vinyl you left around the bounding rectangle.
on the subsequent layers snip an inch or so off of each corner at 45 degrees.
Register each subsequent layer with the inside of the rectangle applied with he first layer. Lining up where the 45 degree cut off corners intersect the edges of the rectangle in the base layer will give you 8 distinct and very accurate reference points for locating each subsequent layer.
When you're all done, remove the border outline from the first layer.
Even using this method more often than not it's faster and every bit as accurate just to eyeball it.