Congratulations! When is the baby going to be here? If the precious bundle is going to be here next spring and the flannel backing is think, you might want to think about quilting it without the batting.
Otherwise, you will notice a slight bump when adding adding another strip of batting to the previous. However, that sweet little one won't care. All that matters is that the quilt came from you.
The love you wrap them in means more than any imperfection.