Okay, so as of now there are four gems in the game.
one in the water, one on the fire/lamp right outside the back door, one behind a pillar outside near the path, and one behind the stone statue.
I couldn't figure out what to do with them until I took them and placed them into the stone hole/basin that is right next to the backdoor fire/lamp. The stones disappear when you place them in this hole, and as of the time posting this, I have no clue as to what it does if anything at all yet, we'll have to wait for the next update.
TL;DR place stones in empty well/hole outside backdoor.