If the batting scrap is big enough to cover a book I might save it. I trash the small stuff. I use an "edge joining foot" & butt the edges together and zig zag without overlapping pieces. I have not been able to detect batting seams inside the finished quilt.
If you are hand quilting, the seams might be a pain to stitch through. I have saved so much stuff over the years. I'm ready to set myself free.