When I sew something with multiple layers I scribe my stitch line on the top piece before gluing up the layers. I normally scribe the line 3/16" in from the edge to provide a little more support.
After stitching, I sand the edges to make all the layers even and then dye and finish the edges. Have to admit that I usually get a bit nervous when stitching holsters that total @12mm in thickness at the edge! If I let the piece tilt just a little or if the needle hits a hard spot somewhere inside the layers and deflects, the bottom stitch can come out the side and that ruins my day!