You need to customize CodeWarrior initialization file C:\Program Files (x86)\Freescale\CodeWarrior PA V8.8\PowerPC_EABI_Support\Initialization_Files\PQ2\8309SOM_init.cfg to make it suitable for your custom board.
1. Please modify Local Access Windows for NOR flash.
2. Please modify DDR2 Controller Registers settings according to your target board.
3. Please modify Local Bus Interface Configuration to configure OR0 and BR0 for your NOR flash.
You could refer to MPC8309 Reference manual for details.
First You could create a bareboard project for MPC8309SOM from File->New->EPPC New Project Wizard, then modify CW initialization file from Edit->Debug Version Settings->Debugger->EPPC Debugger->Use Target initialization, and click debug to check whether the sample program can run on your target board.
At last, in "Program/Verify" panel in "Flash Programmer" you need to check "Apply Address Offset" and specify the address of NOR flash.