I think I would use inexpensive flannel for batting, being sure to laundry first ... I like it sometimes better than warm and natural, especially cuz it is less expensive and has a nice soft hand to it.
With the dark fabric squares, it might be a real challenge to stitch in the ditch without the thread showing on either side of the blocks. How about use a decorative stitch to sew down the center of your seams in a contrasting color? Some machines have a nice big S stitch that works great ... my machine doesn't so I pick an easy one that doesn't use lots of thread.
Sometimes I just use a decorative stitch diagonally thru the squares, (one direction only, or both creating an X ... up to you) changing the decorative stitch on each row ... that might be fun and pleasing to the eye IMHO
warm quilt hugs, sue in CA