Yes. Just set the CPU frequency in the SOPC/CPU configuration and adjust your PLL or external clock to drive at the same frequency. The timing analyser should be used to confirm that you can run at the intended frequency (or what the maximum could be if you decided to increase it).
Know that if you're using the jtag interface (debug or jtag_uart), you're minimum clock frequency has to be ~2x the maximum that the JTAG chain will be driven at (~8MHz). To be safe, you shouldn't go below 20MHz.
