If the batting is W&N, the smooth side is supposed to be next to the backing -- at least according to this prior thread on the QB:
Batting -- is there a right and wrong side??? . I think Nature's Touch 100% cotton is also needlepunched through scrim but I think the scrim is centered so there is no right side/wrong side. I could be wrong about this, though. I rarely use this kind of batting anymore so I would probably Google to get accurate information if I were going to layer a quilt with one of these.
Scrim stabilizes the batting a *lot*, which is why you can quilt W&N up to 10" apart. That is the purpose of scrim -- to create a very stable batting. Vintage style all-cotton battings did not (and still do not) have any kind of stabilization, which is why the recommended quilting distance for those types of batting is 2" or less. When quilting lines are farther apart with these battings, the batting tends to ball up with washing and use and become lumpy.
There are other ways manufacturers stabilize batting (other than needlepunching through scrim). Quilter's Dream, for example, creates very stable battings just by needlepunching (without scrim). Other manufacturers use chemical bonding materials (probably more common with polyester battings) or heat to make the batting more stable. Some bonding processes are mechanical (e.g., needlepunching), some are chemical, and some involve heat. All are designed to make the batting more stable so that quilting distances can be greater than 2" without the batting becoming lumpy over time. These battings typically specify quilting distance somewhere between 2" and 10", with 4" being common.
Wool batting requires different processing to make the batting stable, since wool fibers have little hooks that can cause the wool to irritate skin and/or migrate (beard through fabric). This is one reason to stick to brand names for wool batting (Hobbs and Quilter's Dream). Newer manufacturing processes stabilize the wool batting much better. Before these processes, wool batting needed to be encased in cheesecloth before it could be sandwiched in a quilt (so you didn't get scratchy wool fibers migrating through the fabric creating a bearding problem).
The different stabilization processes result in different characteristics of the batting. Needlepunching through scrim, for example, produces batting that is relatively heavy in weight and stiff in drape. The drape softens over time through washings and use, but the weight remains. A large quilt made with W&N will be much heavier (especially when wet!) than the same size quilt made with QD cotton, or Hobbs 80/20 or a polyester batting. The lofts vary with each of these as well.
Hope this is helpful.