there are BOOT.BIN and image.ub
call C:\\Xilinx\\SDK\\2015.2\\.\\bin\\zynq_flash.bat -f BOOT.bin -flash_type qspi_single
this will update the Flash with BOOT.BIN
note: BOOT.BIN includes: FSBL (first stage bootloader, FPGA bitstream and u-boot)
From flash only FSBL is loaded, then this FSBL loads from BOOT.BIN on SD Card
after that u-boot would load linux image from image.ub
note: it is possible that terminal does not accpept input, please close and open putty, this should help, there seems to be a issue that some terminal program go nuts if the say some garbage during FPGA config. We are working on this..