If possible, I would replace the fabric pieces. If you carefully pick out the seams with your stitch ripper, most of the time you can get a new piece in without too much trouble. If that is not a viable option, I would fuse a matching piece of the fabric under the fabric and see how it looks then. Perhaps then quilt well over the mended area? You could add an applique or embroidered piece over the mend if you could get something that you liked also. I'm so sorry that your top has some problems.