Hi Luca,
1. There is not a supported driver for the AD9643 eval board on the Xilinx Zinq board. The FPGA would need to be programmed accordingly keeping in mind the pinout from the AD9643 evaluation board. There are similar boards that have been utilized with the Xilinx Zinq board which you can see here: http://wiki.analog.com/resources/alliances/xilinx?&#ad-adc-fmc_adapter_board
2. The CVT-ADC-FMC-INTPZB is suitable to connect the AD9643 eval board to the Xilinx Zinq board (referenece comments on pinout from 1 above). It will mechanically connect, but care needs to be taken on the pinout compability.
3. The analog inputs to the AD9643 device itself are differential. The evaluation board has a single-ended input that is converted to differential on the board via the double balun input network. You only need to input an analog signal from a single ended 50 ohm source. Please reference the User Guide or Quick Start Guide found at: AD9643 Evaluation Board | Analog Devices
Best regards,
Jonathan