Scrim side down, against the backing. When there's no scrim, it's smoothest side down, against the backing.

Directly from the Warm & Natural mfgs site:
https://warmcompany.com/content/faq
"...the cotton side facing towards your quilt top and the scrim side facing to your quilt backing..."

That makes sense to me ... The "fluffy" side will be up, for the best appearance after quilting.

This really only makes a difference when quilting on a longarm or extended throat sit down that uses the bigger size specialty needles. The larger needles will make pokies of batting come through to the backing if you have it loaded the wrong way.

If hand quilting or quilting on a domestic the problem never arises due to the much finer size of the needle.

But, be careful if your quilt top has any thin, white fabric. The "cotton" side of W&N is the side with the little flecks of organic material in it. These can show thru thin white fabric. Ask me how I know .....!

I mostly use polyester batting. Some have a smooth side and I use that against the top. When I use W&N I try for the same. Most important is it is warm and pretty. I give away most of my quilts.

Someone told me "Pimples up, dimples down"

Never thought about that before. Great point!

I never gave this much thought so thank you everyone for the info. I'll pay more attention now

Poly batting may scrub the fabric over time causing it to thin and fray. I use it for a lot of utility quilts but not for a quilt I would like to last for a long time.