Baking side of pizza stone
Many pizza stones are double-sided, if so you can use either. If you have a big difference between the two surfaces then I suggest using the smoother one. 

Pizza can stick like glue to a baking stone, if you liberally sprinkle fine cornmeal, or better yet medium ground semolina under the dough it will keep it from adhering to the surface. 

Also be sure to pre-heat the oven a long time before baking to get the stone up to temperature. An inch of stone takes well oven an hour to be ready to bake on.