I don't think you would hurt anything by adding additional clay on top of the bentonite. I just finished up patching a rocky area in my pond that I believed was leaking. What I did was remove dirt over the rock, applied bentonite in power form and covered it back up with dirt. I then used my disc to work some in on top of the dirt too and pack best I could with my tractor. Then I pulled in clay from above the leak for added protection.
