It could be that i did not understand your question very good but: The DE2-115 has 2 SMA connections, one for clock in and 1 for clock out. You can use these. If your clock frequency is on te low side you could also use a GPIO pin to connect the clock to a simple digital input of the fpga. I would advise to use this clock signal to drive a PLL and then use the output of the pll to do the rest of the job. Best Regards, Johi.