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.

I think unless you are hand quilting or have a problem with bearding (when the batting pokes out the needle holes and shows against the fabric) it doesn't really matter. It doesn't make any difference in how the quilt feels once it is complete.

:oops: I'm embarrassed to admit that I've never used any other batting but the one from WalMart. I use the traditional-type poly. I've just got to step out of the box and get some of that Warm and Natural or the Warm and White. This is an interesting thread.