In addition to the previous: I just realized this is a Codewarrior forum (entered here from a Google entry). My problem was actually the same, Codewarrior replaces any programs on the flash memory; so my solution should help you. The CFFlasher programmer I mentioned is provided with the EVB on SBCTools CD, also it's available here on this freescale.com site. And when you are using M5208, remember to upgrade the tool to supply this processor (upgrade is available separately).
If you haven't bought the Codewarrior yet, and you are going to develop software to uClinux, I recommend you to use the SBCTools environment instead of Codewarrior, just because it's free.