I do it backwards.
Put the BATTING on the floor or table. Smooth it out. (The batting seems to sit still better for me.)
Lay the BACKING on top of that. (I find I get the wrinkles out of the backing better when I can see it.) Pin as needed.
Flip it all over and put the top on. Smooth it out and pin.
You can then remove the pins from the backing that only went through the batting and the backing.
This also works very well for me with spray basting.