ive backed more quilts than i can count with flannel- it is one of my very favorite fabrics!
just pre-wash it and dry it- (i've been using flannels for 45+years and only pre-wash once- not 2 or 3 times- i've never had an *adverse* effect)
i toss it into the washer on a warm -regular setting- then i toss it into the dryer (flannel is a looser weave and will fray more than regular cottons- that's why its so good for raggy quilts) so you can either *use pinking shears- or zig=zag or use a serger* on the cut edges- to help control the fraying or even place the yardage in a large mesh bag-
i most of the time don't bother- i deal with the tangled mess of strings when it comes out- but some folks tend to really freak out when they see those-so you might want to (spare yourself the trauma)
flannel quilts up beautifully- and each time the quilt is washed/dried it will only get softer/cozier- and oh so nice.
choose a good quality flannel- fairly heavy- i use double napped benartex flannels most of the time- moda's *woolies* flannels are also wonderful.