I always pre-wash flannel because it shrinks unevenly and seems to bleed more often than other cotton fabrics. When constructing the quilt, I use three layers of flannel with no batting, sometimes mixing in some corduroy, so I don't have to quilt an X through the squares and all 3 layers of flannel produce more fraying. Be sure to make your seams 1/2" or larger instead of the traditional 1/4" when making a rag quilt.