Yes ,flannel can be used for the center of a quilt. Some quilts even omit the center of the "sandwich" depending on the weight desired or simply by neccesity and style. Crazy quilts usually had little, if any, center layer. I agree with Moonpi.....I don't know of any who have lost toes or fingers to quilts that are tied. I daresay, as long as the stitch isn't over a 1/4" and is snipped close, it should present no problem. Basically you are tacking it down. I do know buttons are an absolute no-no.