I'm not sure exactly what you are asking.
Partial reconfiguration has both a full configuration bitstream and one or more partial bitstreams that can reconfigure a isolated portion of the design, while the rest of the design continues to function. This doesn't require a special control unit, unless you are intending to do the partial reconfiguration from inside the FPGA with ICAP. AFAIK if you are using Zynq you can perform the partial reconfiguration from the ARM too.