A Zynq board isn't all that different from your router. When it powers up, the CPU reads the bootloader, typically u-boot, from somewhere and starts running it

A Zynq board isn't all that different from your router. When it powers up, the CPU reads the bootloader, typically u-boot, from somewhere and starts running it. The bootloader then reads the kernel from somewhere, maybe a ramdisk too and starts running Linux. The only difference with the Zynq is that before jumping into the kernel the bootloader will read the FPGA bitstream from somewhere and reconfigure the chip. The design of the board itself will tell the CPU where to look for the bootloader, the location of the files for subsequent stages will come from what defaults had been compiled into the bootloader or from an external config file. If you are already comfortable with cross-compiling Linux then you can just build a kernel from the official tree [1] and add it to the sample SDCard image. You may as well download the Xilinx SDK to get a pre-built cross-compiler. One thing that I find helps is to have a SDCard reader/writer for the desktop or laptop that I'm using as my development machine. [1] https://github.com/Xilinx/linux-xlnx https://github.com/Xilinx/linux-xlnx