If you are doing fusible applique you can use sharpie pens for the signature. The process of fusing the leaves will also set the sharpie. Tartan is correct about the applique being done on the top before the quilt is sandwiched and quilted. As far as quilting applique, that is a matter of personal preference but traditionally applique is outlined with minimal, if any quilting done on the applique itself unless it is very large.
Here is a link to a google search I did that would show you examples of how much quilting can be done, or not done, on applique.
https://www.google.com/search?q=quil...jQDSkQ_AUIBygC
Myself, I always ditch applique and I usually quilt vein lines on a leaf.