Another possibility, at least in CodeWarrior (haven't tried in KDS yet) is to set up a target task to load the bootloader into flash separately. I do that for development, and in production we use a P&E Cyclone ACP that's configured to install both images.
With the bootloader added under 'other executables' it's easier to debug bootloader issues, too. I'm using my own fairly hefty C bootloader, though. Hopefully if you're using a vendor-provided one you won't need to debug it!
Scott