There are basically 2 ways how to program S12Z in CodeWarrior(Eclipse):
1) via Debug Configuration (Assume you are using Pemicro debug probe)
2) via Flash programmer (Target Task configuration)
Another way is programmer which is provided by www.pemicro.com or another company.
If you use option #1 I'd suggest to consider program the device using Target Task. Simply create a new target task, configure the flash memory and programming sequence.



You can also execute Target Task scripts from the debugger console.
Hope it helps.