LEVIATHAN'S GORGE (THE KINGDOM OF THE DEAD)
1) You can find the stone under the bridge pictured on screenshot 1, located in the central area of Leviathan's Gorge; however it's quite a challenge to get it. To reach the areas below the bridge, use interactive ledges and other handholds located in the ruins north-west of the bridge (screenshot 2).
Your destination is the place illustrated on screenshot 1. Use interactive ledges, assisting yourself with Death Grip when necessary. On your way you're going to have to land on a side ledge with shadowbombs, and use them to pave your way to the next passageway (screenshot 2).
After you reach the last but not least ledge (screenshot 1), stand on one of the pressure plates and activate Soul Splitter. Send the first half to the second pressure plate, and the second one over to the last ledge. Use the second half to grab dormant shadowbombs (screenshot 2) and destroy all yellow crystals in the area.
Stay on the last ledge (don't end Soul Splitter too early!) and look at the ceiling to find the stone hidden on it (the above screen).
ETERNAL THRONE (THE KINGDOM OF THE DEAD)
1) You can find the stone in the room beneath the balcony on which the Chancellor is standing. Take the stairs pictured on screenshot 1. When you reach the basement (the one with the Serpent's Tome and a lot of destroyable chests), look around for the secret pictured on screenshot 2.
BREACH (THE KINGDOM OF THE DEAD)
1) You can find the stone on the outside balcony on which there is a statue with a lantern (screenshot 1). The access to the balcony is initially blocked. The walkthrough detailing how to reach the balcony and open the grates to the statue can be found in the Additional Locations chapter, under the The Breach - Exploring The Breach and The Breach - Exploring the ruins sections.
CITY OF THE DEAD (THE KINGDOM OF THE DEAD)
1) The stone can be found while going through the upper levels of the City of the Dead, as soon as you stop running from the burning lift and enter the area where you fight powerful monsters on separate arenas. When you win the first duel, face the north tower and you'll see the secret in the distance.