One thing .. I do not use pins much when sewing flannel ( a plus) . It just clings to itself . This can be a bit problematic as the fabric will not "move" on itself sometimes when you would like it to. There is not much sliding one layer on another layer, you have to pick it up and re-position.
Do preshrink! Let the fabric really soak in the water to fully saturate the fibers ( soak over night). Then spin and put in the dryer until it is completely dry.
Clean your rotary mat and cutter frequently.... and the bobbin area of your machine. FYI - I find it really a big pain to take out stiches in flannel since they sink into the fabric more than a regular quilting cotton.