What I would do is; pick a fabric for the top that goes with the rest,larger than the hole, batting large enough to fill the hole, and backing fabric a little larger than the hole. I'd start with the backing; hand sew your patch, whip stitch the batting , then add the top patch, by hand,I use the back sides of fabrics sometimes if I want a faded look.
Don't worry, with a little patience, and some hand work it'll be fine.
Good luck