Efficient processing of fine-pitched Through Silicon Vias, micro-bumps and back-side re-distribution layers enable face-to-back or face-to-face integration of heterogeneous ICs using 3D stacking and/or Silicon Interposers. While these technology features are extremely compelling, they considerably stress the existing design practices and EDA tool flows typically conceived for 2D systems. With all system, technology and implementation level options brought with these features, the design space increases to an extent where traditional 2D tools cannot be used any more for efficient exploration. Therefore, the cost-effective design of future 3D ICs products will require new planning and co-optimisation techniques and tools that are fast and accurate enough to cope with these challenges. In this paper we present design methodology and the practical EDA tool chain that covers different aspects of the design flow and is specific to efficient design of 3D-ICs. Flow features include: fast synthesis and 3D design partitioning at gate level, TSV/micro-bump array planning, 3D floor planning, placement and routing, congestion analysis, fast thermal and mechanical modeling, easy technology vs. implementation trade-off analysis, 3D device models generations and Design-for-Test (DfT). The application of the tool chain is illustrated using concrete example of a real-world design, showing not only the applicability of the tool chain, but also the benefits of heterogeneous 2.5 and 3D integration technologies.