I have made a few of these as well and all but one I used leftover batting scraps from other projects, making sure each square of batting was similar to others in content and loft. Sew an X across each square to keep it in place. Although on one I did, for my DGS, I quilted a different design on each square that mimic-ed the fabric. Some had stars, some hearts, some were cross-hatched, etc,..
Looked really neat when done. Can't wait to get a few WIPs done so I can make another one that has different quilted motifs in each square like his.