Your quilt your way. Kids love different textures and I have mixed flannel, regular cotton and fleece. As has been said before -- definitely wash the flannel (twice is good, but at least once and dry hot). My first flannel quilt had several different flannels, I did not wash them and they all shrank differently when washed. What a mess!! I just had a piece of LQS flannel shrink 4" in width. Also, the flannel tends to shed more than regular cotton so getting all that shedding over first so it does not stick in the bobbin or on the needle bar puts you ahead of the game.