Extra ingredients will be left in the cube and returned to you when the Cube window is closed. They are not pulled directly from the inventory or stash. The only way to access it is by clicking the cube, or Zoltun Kulle standing beside it in town.
Click it and it will return to town and can be used indefinitely on non-Season characters.
Make your way through the Elder Sanctum until you find it. The Cube is typically found in the Elder Sanctum which is located in the top right, lower left or right of the Ruins of Sescheron. To find Kanai’s Cube, obtain it from the Ruins of Sescheron (Act 3) in Adventure Mode.