I know this is can be a very dumb question, but how do you layer elements on top of each other?
Use the prop tool to set the x and y of multiple particles to the same value. When checking that you have layered them successfully, use ctrl-right click instead of right click to delete only the topmost particle of the stack.
It does not work.
You can just use PROP tool and set both X and Y value on the same number, so both pixels will "stack" on each other.