Hi,
To program external QSPI you should select proper algorithm within CodeWarrior debugger or P&E Micro programmer. You did not specify the CW version you are using.
For example in CW10.x algorithms should be located in
[CW10.x installation]\MCU\bin\plugins\support\EPPC\gdi\P&E\Spansion_*.PCP".
You can use one of these algorithms in "Debug Configuration" \ "Connection Configuration dialog" (see attached screenshot).
The AN4777 deals with using the QSPI module on MPC564S so you can refer to it.
See http://cache.nxp.com/files/microcontrollers/doc/app_note/AN4777.pdf and
http://cache.nxp.com/files/microcontrollers/doc/app_note/AN4777SW.zip
BR, Petr