What stones can I put in the bottom of my new pond?

It's best not to put anything in the bottom of the pond, except pond plants already settled in a planting basket. You can add gravel to the top of the baskets after planting, and this may help to keep fish from rooting around in them, but this is best done to baskets on the planting shelf, where the top is quite near the surface, not at the bottom of the pond. In time a natural pond sludge will form at the bottom, and this is beneficial to many hibernating creatures such as frogs and insects. Adding stones of any kind is unnecessary and may damage the liner when, in time, you need to dredge out some of the sludge if it's getting too much. Let the pond plants settle and begin to grow away before adding the fish, as otherwise they may pull the unrooted stems out of the planting medium.