first ATC, I've been wanting to make a practical, useful version.
If you have difficulty lining up vinyl, here's what I do. After weeding out the unwanted vinyl, I peel back the wax and cut some off, leaving part of the adhesive exposed. I hold the vinyl (waxed area) and paper against the light. This lets you see all the layers to center the circles. Once you like the placement, press the sticky area and remove the remaining wax - and voilà, centered circles!
My 3D owl box is now available in my shop. Hope you have a hoot making these!