The rough side of batting should always go against the quilt top. The smooth side goes against the backing so your needle doesn't push cotton through to the back. If you are using a dull needle, though, that will happen even if your batting is correctly positioned.

I washed and dried the batting. I didn't even use a pillowcase. I put it on the handwash cycle using hot water and bleach (!!!) and then in the dryer for a loooong time because it kept rolling up. I was washing 2 pieces about 58 by the width of the batting (90 I think). It came out just fine. I still put the smooth side up for the lighter colored quilt but will do it smooth side down for the other quilt I made, which isn't so light colored.

I always use W&N and have never had a problem with the batting showing through light fabric.

I have moved to warm&white because of the plant material that is included in W&N.

your plan sounds fine to me. I've never washed the W&N before quilting. Glad to know it works. I have also switched to just using W&W.

I use warm and natural batting a lot and have never had these black spots you are referring to. Is it possible that yours is defective? I hope everything works out for you.

Update: I did the quilting using a Janome purple tip needle and there was no bearding.

Update again. Even though I pre washed and dried the fabrics and batting the quilt still got that puckery look after washing. Maybe because of the thread? There isn't a lot of quilting on it but I have another I'm working on with a lot more quilting so we'll see. I don't mind the puckery look but was kind of hoping that since almost everything was prewashed it would stay more smooth this time. I can't really prewash thread and all of my fabric is washed.

I have often wondered if cotton thread shrinks?