All calculations for devices (earlier also called two-probe systems) in ATK are done using the NEGF formalism, in order to treat the electron transport at finite (and zero) bias. In this case, open boundary conditions apply in the transport direction (Z), as opposed to the periodic boundary conditions used in traditional electronic structure codes.
You will be able to find a bit more background information on NEGF in the Reference Manual of the new 12.2 release, coming very soon, but I recommend you to have a look at the methodology papers listed at
http://quantumwise.com/publications/scientific-publications (section on "Background material").
Yes, you can apply a vertical electric field by inserting metallic regions above and below the structure, and apply a voltage difference between them. In this case it is important to use Dirichlet boundary conditions in the direction of the field, and of course periodic in other directions. Just don't try it for single-layer graphene, there appears to be no effect at all. But bilayer - that's interesting!