I've made flannel pieced quilts that have lasted 20+ years, flannel is a soft, cozy cotton fabric. I use good quality flannels, not thin loosely woven flannels. I construct a quilt the same as I would using any other cotton fabric. I mix flannels and regular cottons in quilts, they turn out just fine. I press seams to one side unless there are multiple seams coming together, ( star points,pinwheels) or when instructions recommend pressing open. I use the regular seam allowance unless the fabric is fraying a lot, in that case I cut my pieces larger -add the excess seam allowance- so I can use 1/2" instead but still have blocks come out the correct size.
I free motion quilt my flannel quilts, flannel quilts beautifully! Your batting choice determines if tieing vs. quilting will work. Some battings are Not ok to tie the quilt. But, no reason to not quilt the flannel quilt.