Now you can manipulate the one leaf without harming any of the other layers.
So size it to where it looks about the same size as the leaf under it.
Go over to the tool options click apply.

Now your image should look like this.

Now we are going to apply an inner bevel to this leaf.
Go up to Image, Effects, Inner Bevel.
A window like below will pop up. 
Put your settings as I have them.

Click ok.
Now Go to Layers, Merge all visible. 
Your finished. 

Your finished image should look something like this.

I hope you enjoyed this tutorial.