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We are motivated to model PE-CVD (plasma enhanced chemical vapor deposition) processes for metallic bipolar plates, and their optimization for depositing a heterogeneous layer on the metallic plate. Moreover a constraint to the deposition process is a very low pressure (nearly a vacuum) and a low temperature (about 400 K). The contribution of this paper is to derive a multiphysics system of multiple physics problems that includes some assumptions to simplify the complicate process and allows of deriving a computable mathematical model without neglecting the real-life processes. To model the gaseous transport in the apparatus we employ mobile gas phase streams, immobile and mobile phases in a chamber that is filled with porous medium (plasma layers). Numerical methods are discussed to solve such multi-scale and multi phase models and to obtain qualitative results for the delicate multiphysical processes in the chamber. We discuss a splitting analysis to couple such multiphysical problems. The verification of such a complicated model is done with real-life experiments for single species. Such numerical simulations help to economize on expensive physical experiments and obtain control mechanisms for the delicate deposition process.