The Device ID and Vendor ID can not be changed.
Typically the bootrom would write the Subsystem ID and Subsystem Vendor ID by doing a config write to the controller cfg space.
For PCI, just write the desired value to offset 0x2c.
For PCI Express, write offset 0x478 and then set the ready bit in 0x4b0.
Search for "subsystem" in:
http://www.freescale.com/files/32bit/doc/ref_manual/MPC8548ERM.pdf-EdS