A system and method is disclosed in an emulation environment that dynamically remaps user designs. In one embodiment, a request is received to load an integrated circuit design to be emulated in a desired partition within the emulator. The emulator automatically determines the availability of the partition requested. If the partition is not available, the design is dynamically remapped to a different partition that is available. In another embodiment, clocks associated with the integrated circuit design are also dynamically remapped. In yet another embodiment, the user can control the size of the partitions (e.g., the number of printed circuit boards in a partition).