For more information of the final processing of an OS image, see mkrec in the Utilities Reference.
Many boards have a ROM monitor, a simple program that runs when you first power on the board. The ROM monitor lets you communicate with your board via a command-line interface (over a serial or Ethernet link), download images to the board's system memory, burn images into flash, etc.
The QNX System Builder has a TFTP server that you can use to communicate with your board.