I love,and make, lots of flannel quilts. My favorite flannels are Benartex and Moda double side flannels ( both sides are brushed, soft, very substantial good quality flannels. I've never had a problem with colors running. I do prewash ( gently) in warm water, dry to just barely dry. Starch & iron before cutting. Nice, sharp New blade in the rotary cutter. I use a normal seam allowance unless making raggy quilts. Prewashing helps tighten up the weave so fraying isn't that much of an issue. I always use batting in my flannel quilts. They are so wonderfully soft, lofty, cozy.