Custom Flash is not supported in Altera Qsys 12.0

OK, if Flash pins are not shared, "tristate conduit pin sharer" is not needed.

Flash presets (Quartus 12.0SP1) didn't make me happy ;-)

Flash memory must be taken as memory in BSP

In qsys-edit, flash memory generic .... component editor, check :

(this is an example)

in module_assignment :

embeddedsw.configuration.hwClassnameDriverSupportList = altera_avalon_lan91c111:altera_avalon_cfi_flash
embeddedsw.configuration.isMemoryDevice = 1
embeddedsw.CMacro.SIZE = 4194304 for my 4MB
embeddedsw.configuration.hwClassnameDriverSupportDefault = altera_avalon_cfi_flash
embeddedsw.memoryInfo.IS_FLASH = 1
embeddedsw.memoryInfo.FLASH_INSTALL_DIR = APP_DIR

in interface_assignment :

embeddedsw.configuration.isMemoryDevice = 1
embeddedsw.configuration.isFlash = 1
embeddedsw.configuration.isNonVolatileStorage = 1
embeddedsw.configuration.isPrintableDevice =0
embeddedsw.CMacro.SIZE = 4194304
embeddedsw.CMacro.SETUP_VALUE = 65
embeddedsw.CMacro.WAIT_VALUE = 100
embeddedsw.CMacro.HOLD_VALUE = 30

After generating Qsys, you will be able to select "altera_avalon_cfi_flash" for flash in BSP editor.

EDIT : Good Luck