AD-FMCOMMS1-EBZ and AD-FMCJESDADC1-EBZ are different boards.
I am guessing you are asking about FMCOMMS1.
The FFT core is just an offline FFT module - because this core can not meet the bandwidth of ADC.
If your FFT module is exepecting raw samples and is capable of running at 250MHz throughput (2 samples per clock) you can simply connect the ADC to it.