When I quilted with my dm I put the cleaner side up against the top of the quilt and after getting my HQ16 read that the side with the stuff? dirty side is up, so that is how I now load the batting every time, using WN.
With warm and white I did run into a problem with pokies one time, could have been the fabric (is was a customers). I turned the batting over and never had the pokies again; so with the warm and white the patterned side goes up against the top.