It isn't always easy to know if a patch needs to be lined. The simplest way to determine this is to place a piece of white paper or a piece of white cotton fabric underneath a portion of the design. In our example, it is the dark background fabric that is showing through.
It is not always the background that is dark. You may be building a flower with many petals. Those petals may become lighter as you build layer upon layer. You may reach a point that a darker petal shows through a lighter petal. If so, test your fabric with the white paper or white cotton to determine if lining the patch will improve the appearance of your appliqué and hide the seams.