yes you should pre-wash your flannel- some people insist on pre-washing flannel 3 or more times---i never do- i've been using flannels for over 40 years- i love flannel! and back many quilts with it- i incorporate it into the tops of quilts- i use flannel when ever i feel it is the right choice for what i am doing- i pre-wash ONE time-- batting and quilting have as much (and more) to do with final results as the fabrics do--
flannel has a looser weave than the regular cottons we use- pre-washing tightens up that weave giving you a more *luxurious* soft/fluffy fabric with good body. and makes wonderful cozy quilts!