Applique is generally done before sandwiching, but not always. It's easiest to do it before layering, but there are some people who applique & quilt all in one step.
http://www.quiltingboard.com/main-f1...e-t195933.html
I would definitely
not send any instructions other than to sign. People's irons will be different & a lot of people will try to cut things out with dull paper scissors. We tried having quilters who knew nothing about applique in our guild try to follow basic instructions and ended up with melted & burned applique pieces & some pieces that were too small. Also, realize that some people will lose their leaves so you'll need extras on hand. Sharpies will work fine. If you care about color, be sure to tell people or you will get people that try to sign in pink and gold or a different color for every letter of their name. And you want to let them know to sign in the middle so their name doesn't get lost in the stitching/turned edge.
I wouldn't attach anything to the fabric before mailing because it will end up peeling off and/or people will peel it off not realizing its purpose. You can run a dry iron over the signed fabric no problem. For the quilting, I'd just quilt around the edges for the signed leaves. If you want to add blank leaves, you could add quilted veins inside those.