Use your hammer to fragment a section of a tile. Your goal here is to fracture the surface so it will flake out, allowing you access to the substrate beneath the slate.
Use your prybar to get underneath the bottom of the slate tile. Ease the edge of your prybar underneath and apply pressure. Some tiles will be easier than others, so you will be applying varying degrees of force.
Repeat the process, using your hammer if necessary to drive the prybar under the edge of the slate. Most of the tiles will simply flake up once you get the edge of the bar underneath, but sometimes it requires a little excess force to get the prybar under the edge.
Use your hammer and chisel for areas where the slate tile is more difficult to remove. Thinset mortar is concrete-based, and if the installation was done properly then the thinset will likely require some additional effort to remove.
Work your way out from your starting point until you are done.