The Vitis Unified IDE has a feature for programming the board/part using JTAG. You can bypass copying the contents of sd_card to an actual SD card for booting on the board.
Programming Flash
After successfully building a System Project for hardware, select Program Flash from the Vitis menu.
In this screen, specify the Image File,
which is generally the BOOT.BIN. Specify any
offset, if necessary for the flash memory. Specify the Init File. The Init File is the partial PDI from the platform you
are targeting.
To make sure the flash is programmed properly, check Verify after flash to confirm proper programming. If the flash memory already has existing data, you can perform secure erase by checking the Blank check after erase check box.
Make sure that the Packaging options in
the System Project Settings window has set
--package.boot_mode=qspi.
Programming the Device
If you only want to program the device through JTAG, select Program Device under the Vitis menu.