The atoms are manipulated by a scanning tunneling microscope [1], which allows you to both image and manipulate single atoms, as shown in the movie "A Boy and His Atom" [2], also made by IBM. You can make sure there's only one by just taking an image at a resolution high enough to see single atoms.
This is fundamentally a scanning technique. A very sharp tip, down to a few atoms at the point, sometimes capped with a single carbon nanotube, is scanned across the surface of whatever sample you have, which for a measurement like this, must be almost atomically flat. A bias is applied between the sample and the tip, and quantum tunnelling can allow for electrons to move between the sample and the tip. This current can then be measured, and correlated with sample height or electronic properties of the sample. If you scanning step size is less than that of the size of an atom, you can then image single atoms by detecting the change in current due to a different species of atom, or due to the change in height between your flat surface and tip when an atom is sticking out of the top of the surface.
To manipulate the atoms, the tip is moved close enough to an adatom that it begins to form a weak bond with the tip. The tip then can move and essentially drag the adatom with it to wherever the researchers want. [3]
