When laying a new tile floor, do you install the pedestal sink over the tile and if so how do you install the bolts in the floor without cracking the tile?

You install it over the tiles. Bolts are not necessary. Use caulk instead. If the sink is installed properly - bolted to the back and caulked at the back wall, it should sit tight on the pedestal. Caulking between the floor and pedestal should be sufficient.