Due to the increasing pressure to develop small-size and low-cost after-treatment systems meeting the legislative demands it is desirable to integrate multiple functionalities and exploit any possible synergies. Typical examples include DPFs catalyzed with deNOx catalysts, as well as LNT-SCR combinations using layered coating technology. The present paper deals with the modeling challenges involved for the proper simulation of such advanced concepts. Key role in such advanced simulation attempts has the coupling between diffusion-reaction phenomena, which is captured through intra-layer modeling. All investigations in this paper deal with the application of possible combined LNT-SCR system configurations. The simulation results show that a dual bed LNT- passive SCR configuration offers substantial NOx emissions reductions compared to a single LNT catalyst and effectively controls secondary NH3 emissions produced during LNT regeneration phases. The much more compact dual layer system offers potential for less ambitious NOx reductions, however its operation characteristics are more complicated and strongly affected by the diffusion processes inside the washcoat.