If you are using a custom board, as a first step you must to be able to debug a project using a board-specific init.cfg file. Furthermore, "Verify Memory Writes" must be checked in the project's EPPC Debugger Settings panel. Once the debugger can step and run through the main code on the board with Verify Memory Writes on, you can build the ROM version of the project and program the flash.
You can specify a hardware reset configuration word (HRCW) for debug purposes in project settings Remote debugging->CodeWarrior USB TAP (or CodeWarrior Ethernet TAP)->Edit Connection->Use JTAG configuration file, with examples and guidelines in the CodeWarrior installation folder>\PowerPC_EABI_Support\Initialization_Files\jtag_chains. Please use the 8360_rev2_HRCW_jtag.txt file from this folder as an example.
You can program the binary file containing the HRCW with the CodeWarrior Flash Programmer.
To change the value of an existing HRCW (you can use your evaluation board for this procedure) you should follow the next steps:
1. Save the Flash Sector containing the HRCW to a binary file (usually the first sector)
2. Modify using a hex-editor the HRCW in the above file to the desired value
3. Erase that flash sector using the Flash Programmer
4. Re-flash the flash sector with the modified binary file
5. Reset the board
I hope this helps.