To get this to work you will have to make it so you can switch from the ce pin on the nor chip on the board or the ce bin to the nor chip on the motherboard. This is how the nor chips activate and how you get dual boot.
So in close you will need to figure out a switch that can connect to ce pin to the motherboard of the on board flash and also make it so you can connect the ce pin to the motherboard on the dual boot board. I would do this with a three way switch. have the ce pin to the cpu in the center and then have each ce pins on the sides.
also will have to figure out a way to way to read and flash the on board. IF someone was to make the perfect system they would make it so one could connect to the board you have up there to a progskeet or a hardware flasher and then with a switch one could read or write to the flash on the motherboard and then flip it the other way and read and write to the flash on the motherboard.
Thanks is this what you are looking for. If you want someone to test this out once it is all ready to go let me know. thanks