I would say not to layer it with rocks. I have tried it both ways, and
prefer it without. BTW, this is an extremely inflammatory question for
ponders. Don't be surprised if you get both polite and not so polite
responses and even emails on the topic. Do what you want, but if you
decide on doing the rocks, learn as much as you can about the best size
to use, and only make the layer the thickness of a single rock.
You don't mention your filter. I take it that you are not an
experienced ponder. Did you get the pond with a new house? What kind
of filtration do you have, and how big is your pond? If it is an
irregular shape, just give us the longest and widest points and the
depth. What kind of fish were in it, assuming there were some. Are
they now in some kind of temporary tank, or did they die?
Too many questions for me to think of all of them. Just tell us
anything you can think of to help us advise you.
Good luck, enjoy it,

Ann