Modern embedded systems development poses new challenges to a designer due to the global reachability of the contemporary market. One product shipped to different countries or customers should satisfy varying conditions, standards and constraints. Variability of a developed system should be taken into account by a designer. In a case of the embedded heterogeneous systems, this problem becomes challenging. Along with the variability heterogeneity of a system introduces new tasks, which should be addressed during design process. In this work, we propose a technology independent design flow. The proposed solution is supported by state-of-the-art tools and takes into account variability, partitioning, interfacing and dependency resolving processes. This thesis is conducted as a case study. We explored a design process of an industrial project, identified existing challenges and drawbacks in the existing solutions. We propose a new approach to a design flow of heterogeneous embedded systems. Also, a tool, supporting the presented solution, is implemented, which would allow a developer to include this approach into everyday design flow in order to increase a development speed and enable a task automation.