Lay out the locations of the cinder blocks, before drilling any holes into the flagstone, to ensure that the holes you will be drilling fall within the outlines of the central holes in the cinder blocks. Drill 3/8-inch-diameter holes vertically down into the flagstone with a hammer drill. Drill a hole every 16 inches, enough so that a bolt extends into each cinder block. Drill the holes approximately 4 inches deep, which will leave about 6 inches of the bolt protruding from the flagstone foundation.
Spread epoxy over the threaded ends of 10-inch-long steel bolts and fit them into the holes in the flagstone.
Spread mortar over the top face of the flagstone foundation with a trowel.
Place the cinder blocks on top of the flagstone, with the bolts protruding into the interior holes of the cinder blocks.
Fill any of the holes in the cinder blocks that have bolts in them with mortar and pack the mortar tightly around the bolts.