Chao Container #1
The first Chao Container can be easy to miss. At some point in the level you will have to run down a long slope, with an optional series of three ramps which propel you into a lightning shield. After this, you will have to climb a long set of stairs with three enemies in a triangle formation. The Chao Container is hidden on a small alcove above and to the right of the doorway; you will need to climb on a wooden box to get to it. Note, on the Dreamcast version, the layout is slightly different and the Chao Container will be one platform down.
Chao Container #2
Farther on in the level, you will come to a very long, twisting staircase with a rail for grinding down it. At the end of this will be a curved slope; run or spin-dash up it, and you will find the second Chao Container in plain sight.
Chao Container #3
Towards the end of the level, you will run down the side of a very, very tall building. When you reach the ground, a set of springs will instantly launch you into the air. Push forward to land on a pole and begin spinning around it. Press the jump button when the red trail is visible to swing to the next pole. Repeat this action to swing to the platform with the third Chao Container.