Large two-stroke marine Diesel engines have special injector geometries, which differ substantially from the configurations used in most other Diesel engine applications. One of the major differences is that injector orifices are distributed in a highly non-symmetric fashion affecting the spray characteristics. Earlier investigations demonstrated the dependency of the spray morphology on the location of the spray orifice and therefore on the resulting flow conditions at the nozzle tip. Thus, spray structure is directly influenced by the flow formation within the orifice. Following recent Large Eddy Simulation resolved spray primary breakup studies, the present paper focuses on spray secondary breakup modelling of asymmetric spray structures in Euler-Lagrangian framework based on previously obtained droplet distributions of primary breakup. Firstly, the derived droplet distributions were assigned via user coding to RANS 3D-CFD simulation of nozzle bore geometries having 0.0, 0.4 and 0.8 normalized eccentricities. Spray secondary breakup then calculated by using the KH-RT breakup model. The simulations compared to a widely used industrial methodology and validated against experimental measurements performed in a unique Spray Combustion Chamber. Furthermore, effects of nozzle eccentricity were assessed under non-reactive and reactive conditions using a computationally efficient combustion solver. The methodology was found to be promising for future implementation of droplet mapping techniques under marine diesel engine conditions.