Ion transport of multi-ionic solutions through layered electrolyte and polyelectrolyte structures are relevant in a large variety of technical systems such as micro and nanofluidic devices, sensors, batteries and large desalination process systems. We report a new direct numerical simulation model coined EnPEn: it allows to solve a set of first principle equations to predict for multiple ions their concentration and electrical potential profiles in electro-chemically complex architectures of n layered electrolytes E and n polyelectrolytes PE. EnPEn can robustly capture ion transport in sub-millimeter architectures with submicron polyelectrolyte layers. We proof the strength of EnPEn for three yet unsolved architectures: (a) selective Na over Ca transport in surface modified ion selective membranes, (b) ion transport and water splitting in bipolar membranes and (c) transport of weak electrolytes.