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In such cases you have to control the board in by your host development system right upon a POR (power-on reset). In this mode you have full control over every every part of the hardware. However, it will take time to set everything up after booting. Notably, the FPGA configuration has to loaded through JTAG each time you load a new program.
For this you have to set the jumpers on your MicroZed board as follows
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This will boot the device from JTAG. The settings of the jumpers will be read only at power-on! Hence, make sure to cycle the supply power after changing the jumper settings. A soft reset (through the JTAG or by pressing the reset button on the board will reset the board but will not sample the boot mode pins connected to the jumpers.