The small hole in the rods lines up with a small hole in the rod bearings. The purpose is to spray oil against the lobes of the cam to lubricate them. Face the holes to the cam side of the engine and the rods will be installed correctly. Are you using full floating pins? If not then why didn't the machine shop assemble the rods and pistons for you? Pressing pins into rods is not a typical home garage operation.
