Here is my 100% Achievement guide for Deliver Us The Moon!
This is obtained during chapter 6 (Tombaugh Facility).
To find the first duck, about halfway through this chapter you come to a huge theatre (With Outward on the main stage as a name)
In the middle of this area on the bottom floor is a flooded tunnel you can enter.
It has an audio log in it, and on the right has a small tube on the floor. Get your ASE friend to go through it and push the first duck out and make sure to collect it.
The second one is after you do the small electric puzzle in the water.
When you push the canister to the end where you see the electric come out of, jump to the platform above, go left and in the previous room.
On the right hand side of this room is the second duck tied to a red balloon.
If you prefer a visual go to 2:24:00 to find the first duck.. Then go from 2:27:30 to see where the second duck is.
Hope this helps!