The instructions say not to wash the flannel first because it will have a more "raggedy" look but I always wash my flannel because, like you found out, some of it is good and some of it may not be so good,and only washing itfirst will let you know that.
I also use 3 layers of flannel but I cut the center layer 2" smaller than the top and bottom layer. That way I still have that extra piece of flannel for warmth but I'm only cutting 4 vs. 6 layers.