Advise on submerged rocks - fish hide outs.

I am thinking of adding some fairly large rocks in a "pile" to provide my
fish with some hide outs.
I have had problems with Great Blue herons and nothing I have done to date
seems to work.
I am reluctant to put the rocks in direct contact with the liner, would it
be Ok to put a layer of padding (probably old carpet) on top of the liner,
under the rocks.

other ideas would be welcome.
ANO