When I use 2 layers, it is usually to get a lot of loft in the quilting, like trapunto, so I use a warm and natural type on the bottom and a thicker batting on top. For the purposes of quilting/warmth, it doesn't matter if the thicker batting is on the top or bottom..batting quilted farther apart makes warmer quilts than batting stitched very densely. Just be sure not to quilt farther apart than the manufacturer's recommendations on the package. I would try a practice sandwhich and see what I liked best, one or the other on top.