I believe the only type of batting that has a right and wrong side is batting that is needlepunched through scrim. Warm and Natural cotton is needlepunched through scrim. Quilter's Dream cotton is needlepunched, but not through scrim, and I *think* this means it does not have a right and wrong side. Other battings may not be needlepunched, but may be treated with glazing, and these also would not have a right and wrong side (these would be polyester battings, I think).
Which batting type and brand are you using? That would tell us whether your batting has a right and wrong side.