My mom and I have had great success with denim squares alternating with squares from old corduroy pants and or drapery or upholstery remnants. The suggestion to cut the flannel backing squares at the same time is a good one too although we have often pieced only the quilt front and purchased enough yardage of all the same flannel to back the quilt with, seaming it in half or thirds depending on the width of the finished quilt that is planned.
I would reccomment using a serger to put the squares together or alternatively using a straight stitch with a second row of narrow zig zag to prevent fraying unless the plan is to have all the squares with the seams outside and delberately frayed fringe edges on each square or circle. They then last longer through many more washings before needing repair, and are usually heavy enough to not need any batting in the middle and still be nice and warm as a TV blanket or summer bedspread or blanket 8)