The transmission will not be shifted. The purpose and effect of the applied gate "voltage" is to apply a shift to the diagonal Hamiltonian matrix elements for the atoms in the central region
not designated as
surface_atoms. This way one can mimic (I would not say simulate since we "simulate"=model the transport properties in a correct way) the effect of a third electrostatic gate on the transmission spectrum.
So, the screening atoms should be the ones not affected by the gate, according to the way you imagine the gate will influence the system.
This functionality is not entirely trivial to use, that is, one needs to be a bit careful with the interpretation of the results. It can however be put to very good use such as in
Q. Yan et al., Nano Letters 7, 1469 (2007). Also you can search our
publication list for the words "gating" and "gated" to find more inspiration.
Finally, QuantumWise is currently implementing a completely new model for simulating gates, which will allow for self-consistent electrostatic modeling metallic and electrostatic gates. This will make it possible to simulate nanoscale transistor structures in a much more realistic way.