Applique is done on just the quilt top before anything else. I would have the tree trunk and branches appliquéd to the background to show where their leaves will go. I would draw my leaf shape on the paper back (with a pencil) on the fusible and fuse it leaf fabric. I would rough cut the leaf shape leaving extra around so the shape edges don't fray from handling. As for signing the pieces, you will need to try different pens to see what works best.