You've been doing it right, no need to change. The scrim side of both W&N and W&W is the flat side,
not the bumpy side.
Look at W&N, the dirty side, the one with the flecks, is the non-scrim (top) side. That's also the side with the bumps. The scrim (bottom) side is whiter and flatter. The Warm Company confirms this on their FQ page.
http://www.warmcompany.com/faq.html
The same holds true for W&W except there are no flecks to make it easier to see the difference. The flat side is a bit whiter, even with W&W.
Bottom line, the flat side is the scrim side. Reminder hint to get it right every time: 'Bump it up'.
Is there a reason you want two layers of batting for your baby quilt? Won't that make it rather stiff and heavy?