The Embedded Tower is on Route 47. After coming out of the Cliff Edge Gate, the first cave after that has two ladders. Take the downwards one, exit the cave and surf west, ignoring the waterfalls. Once you get to the very leftmost part of the route, there's a tiny patch of land with a wall you can use Rock Climb on, and then the entrance to the Embedded Tower is right there.
However, to get Kyogre to appear, you need the Blue Orb, which can only be obtained after getting one of the Kanto starters in Pallet Town, and then going to see Mr. Pokémon on Route 30.
Actually, you also haven't listed that you got one of the Kanto starters, so maybe you only need to do that to get Steven to appear.
Also, for future reference, asking for clarification should be done as comments, not as answers.