This study proposes the use of a novel integrated framework for 2D en route airspace sub-sectorization. The integrated framework combines the multi-commodity flow optimization approach, complex network clustering approach, and Minimum Bounding Geometry (MBG)-coupled Rule-based Approach for boundary design. A decomposition-based discrete particle swarm optimization (DPSO) is used to solve the clustering problem. The output of the flow optimization is used as a guiding standard for the DPSO. Experimentations were performed using the Indian airspace sector to validate the framework and DPSO was run for different maximum number of generations (maxgen). The findings reveal that the multi-commodity flow approach captures system-wide flow operations. Clustering results corresponding to maxgen=100 and maxgen=150 perform best in terms of equitable and balanced distribution of cluster size and traffic load. The MBG-coupled Rule-based Approach leads to compact and convex sub-sector boundary design. Major implications of this research include dynamic adaptability of the integrated framework, increased sensitivity of sector design to network evolution, and a computationally tractable framework. The higher controllability of the proposed framework also offers an increased acceptance among practitioners.