Hi,
The "FPGA Input Clock Frequency" is the frequency which is the input to the clock module of FPGA and the "FPGA System Clock Frequency" is the one coming out of the clock module which decides at which frequency the system should run on FPGA. "FPGA System Clock Frequency" can be greater than the "FPGA Input Clock Frequency". It all depends on the clock module, it can multiply or divide an input clock frequency to generate a desired system clock frequency.