The general rule of thumb is that the scrim goes toward the backing. Here's why:
Scrim is designed to prevent bearding and/or pokies of batting from coming through the back of the quilt. It also gives stability and structure to the batting fibers. It can be a resin (sprayed on) kind of bonding/scrim or a very thin polypropylene layer in the middle or back side of the batting. This layer almost looks like a very fine white sheet of webbing - sort of like Misty Fuse or a dryer sheet. If it's resin bonded (such as some Hobbs Batting)then it doesn't really matter which side, although many quilters like to put the bumpy side up or the waffle smooth side down. If it has the fine layer in it, if the layer of poly is on one side, that side should go down. If it's in the middle, it doesn't matter.
On some battings if you peel a corner apart, you can actually see and feel the very thin poly sheet on one side. Others you cannot.
So, if you know for sure it has a fiber scrim on one side, lay that side downward. Think about the needle punching through - you want it to go easily through the batting fibers and out the other side, with the scrim last so it catches any wayward batting fibers. If you put the scrim on top, it might resist your needle a tiny bit, perhaps cause thread breakage, and sure won't prevent push through of fibers beneath it.
If you don't know for sure if there is a scrim, lay the smoother side downward, just in case.
Sometimes you really can't see any difference between sides, so pick the smoother side to place down, and hope for the best!
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