Numerical simulations of the cardiac electrophysiology in the atria are often based on the standard bidomain or monodomain equations stated on a two-dimensional manifold. These simulations take advantage of the thinness of the atrial tissue, and their computational cost is reduced, as compared to three-dimensional simulations. However, these models do not take into account the heterogeneities located in the thickness of the tissue, like dis-continuities of the fibre direction, although they can be a substrate for atrial arrhythmia [Hocini et al., 2002, Ho et al., 2002, Nattel, 2002]. We investigate a two-dimensional model with two coupled, superimposed layers that allows to introduce three-dimensional heterogeneities, but retains a reasonable computational cost. We introduce the mathematical derivation of this model and error estimates with respect to the three-dimensional model. We give some numerical illustrations of its interest: we numerically show its convergence for vanishing thickness, introduce an optimization process of the coupling coefficient and assess its validity on physiologically relevant geometries. Our model would be an efficient tool to test the influence of three-dimensional fibre direction heterogeneities in reentries or atrial arrhythmia without using three-dimensional models.