Please modify the following section in CW initialization file C:\Program Files (x86)\Freescale\CodeWarrior PA V8.8\PowerPC_EABI_Support\Initialization_Files\PQ2\ep8248_init.cfg according to your custom board.
# Setup the chip selects
# CS0 is 8MB flash at 0xff800000, 32-bit port, no error checking, writable, GPCM, 60x bus, valid
writemmr BR0 0xFF801801
writemmr OR0 0xFF8008B2
# CS2 is board control & status registers at 0xFA000000, 8-bit port size, GPCM
writemmr OR2 0xfff00854
writemmr BR2 0xFA000801
# CS1 is 16MB SDRAM at 0x00000000, 32-bit port size, SDRAM machine, r/w, valid
writemmr OR1 0xff0030c0
writemmr BR1 0x00001841
Then refer to the attached procedure to do flash programming in CW 8.8.