Quality system design on dynamic partially reconfigurable platform needs exploration of a vast and multidimensional design space for (1) selection among implementation variants of hardware accelerators, (2) partitioning the reconfigurable fabric, and (3) their placement on the reconfigurable fabric partitions. This paper presents a novel methodology ISOMER for integrated solution of selection, partitioning and placement for performance optimization. Architecture under consideration is a general purpose processor coupled with reconfigurable fabric that can be partitioned in multi-sized partially reconfigurable bins. Our methodology determines performance-efficient partitioning and usage of reconfigurable fabric. Extensive evaluation illustrates that our methodology is scalable and outperforms state-of-the-art techniques for non-partially reconfigurable architectures.