Clean the slate tile well before setting the toilet in place. Sweep the the tiles clear, and then wash them with warm water and a sponge. You can use a neutral — nonacidic — cleanser specifically formulated for slate if necessary. Make sure all debris is removed, including any excess caulk, putty or other materials.
Seal the slate tiles with a sealant specifically made for slate. Most slate tiles come sealed, but you should check with your manufacturer before proceeding. Let the sealant dry completely before installing your toilet.
Place a new wax ring around the toilet flange in the floor. The wax ring helps seal the toilet to the floor, thus protecting the floor, like a gasket. The flange connects to the toilet drainage system.
Place the toilet over the wax ring and flange, and thread the nuts on the flange up through the toilet base. Use a wrench to tighten them.
Assemble the rest of the toilet and connect the water supply.