In Museum, the capsule sits right outside the reclamation bin next to the Monomat, as well as the Museum Gift Shop at the very end of the level.

In Sewers, to the left of the Melon Grower room, the Bonebox is located within a room with two Corrupted Nullbodies.

In Sewers, behind the Melon Grower room, insert the Purple Key obtained from the Crablet Ambush room. The Bonebox will be located right after you open the door.

In Sewers, the Bonebox is located at the end of the hallway that the Nullrat Bonebox is at the beginning of.

In Warehouse, the Bonebox is high up on the corner of the building that hovers above the Monomat. You can climb up the building to the left of the Monomat to get to it.

In Runoff, jump all the way down the bottom of the pit after where you first encounter the Zombish. The Bonebox will be hidden under a pile of crates against the right wall.

In Warehouse, navigate to the end of the level with the train. Look up high opposite the back of the train against the wall.

In Time Tower, after reaching the level with the Gravity Core, there are two square spaces in the wall behind where you enter. The Bonebox is in the left one when facing that wall. You can surf a Gravity Orb using the Gravity Staff to get up there.

In Dungeon, look up after spawning and climb up the array of horizontal beams. (You might have to use a prop to reach them.) Once at the top you will see the Reclaimation Bin. Continue past it and turn right. Then, jump to the Bonebox.

In Tower, on the top floor there will be a garden with giant balls surrounding it. Use them to jump to the center. You'll find the Bonebox on the corner of the roof of that area closest to the end of the level.

At the end of The Tower level, look outside your elevator, should be on top of the building to the left of the elevator (You can climb the bars behind the elevator)

In Streets, after fighting the first Omni-Roller of the game, there is a tall fence that says "SORRY" at the base of it. The Bonebox sits right behind it. Completing the following puzzle allows you to jump down from the roof to reach it.