Hi TTA,
The good news is that CFFlasher _IS_ able to program the internal flash on your own target board based on MCF5282.
CFFlasher is a utlity written by Freescale in Austin, and published "as is" to the external web. CFF has a configuration system, so that you should be able to set up any internal/external flash for programming.
CodeWarrior for ColdFire V6.3 ships with a flash programming tool integrated into the IDE. Other, Third Party companies have flash programming utilities for ColdFire as well.
Mark