Hi,
1. If on the board is already a working RCW and you can enter in debug (using Connect/Download configuration), you should program the binary generated from QCS to flash memory, using Flash Programmer.
2. If you are not able to enter in debug mode, you can use the default jtag_chain file (.txt with RCW code) or the one created by you, but the switches on the board should be in sync with the setting in rcw (for example the cpu frequency). After this, you should be able to enter debug mode and program the rcw to flash memory as in step 1.
3. If you have an working u-boot, eth connection to the board and a tftp server, you can load rcw binary directly to the flash using u-boot capabilities. More information in this link.
Adrian