We propose a two-layer model with two different axes of integration and a well-balanced finite volume method. The purpose is to study submarine avalanches and generated tsunamis by a depth-averaged model with different averaged directions for the fluid and the granular layers. Two-layer shallow depth-averaged models usually consider either Cartesian or local coordinates for both layers. However, the motion characteristics of the granular layer and the water wave are different: the granular flow velocity is mainly oriented downslope while water motion related to tsunami wave propagation is mostly horizontal. As a result, the shallow approximation and depth-averaging have to be imposed (i) in the direction normal to the topography for the granular flow and (ii) in the vertical direction for the water layer. To deal with this problem, we define a reference plane related to topography variations and use the associated local coordinates to derive the granular layer equations whereas Cartesian coordinates are used for the fluid layer. Depthaveraging is done orthogonally to that reference plane for the granular layer equations and in the vertical direction for the fluid layer equations. Then, a finite volume method is defined based on an extension of the hydrostatic reconstruction. The proposed method is exactly well-balanced for two kind of stationary solutions: the classical one, when both water and granular masses are at rest; the second one, when only the granular mass is at rest. Several tests are presented to get insight into the sensitivity of the granular flow, deposit and generated water waves to the choice of the coordinate systems. Our results show that even for moderate slopes (up to 30 • ), strong relative errors on the avalanche dynamics and deposit (up to 60%) and on the generated water waves (up to 120%) are made when using Cartesian coordinates for both layers instead of an appropriate local coordinate system as proposed here.