If you impose periodic boundary conditions for a 2D system in the out-of-plane direction, you solve the Poisson equation for a distribution of positive (ions) and negative (electrons) charges with periodic boundary conditions, where the period of the electrostatic potential and charge density is given by the unit cell size in the out-of-plane direction.
In the ATK, you may also solve the Poisson equation on multigrid, imposing (non-periodic) boundary conditions such as Dirichlet, Neumann or mixed boundary conditions.