Wash the flagstones with warm water to remove any debris, and allow them to air dry.
Mix the mortar you are working with per manufacturer's instructions, and pour it into the area where you would like to set the flagstones.
Place a flagstone at one end of the mortar-covered area, and press it down into the mixture. Sink the flagstone into the mortar until there is only a quarter of an inch protruding.
Continue to place flagstones into the mortar in this fashion, fitting the sides of each slab a 1/2 inch to 1 inch away from the previous slab.
Use a rag dipped in warm water to wipe away any mortar that might have gotten onto the tops of the flagstones during the placement process.
Allow the flagstones to set in the mortar for 48 hours before walking on the surface.