After further consideration, I have decided to keep the ATmega328 microcontrollers for bargraphs, keypad, and portplate. But instead of connecting them over USB, I will use the Zynq’s SPI interface. This is made possible by the fact that we do not need a lot of bandwidth between the Zynq and these boards, nor a very low latency. As a result, it will remove the need for USB interfaces on the MCU side, and USB hubs on the MPSoC side. The SPI interface will be used both for programming the MCU (In System Programming) and for full duplex communication, using the Zynq as master.