I punch the top layer then use that as a template for the other layers, most stitching chisels will do two layer or at least mark the bottom piece. After that I use small 1" brads in a few holes to line up all the layers. I put the brads through the top layer glue up everything then push the brads down through the other layers aligning the holes, slide all the layer down the brads and they line up very well, you may need to run an awl through the holes while sewing to open em up a bit.