It would be very helpful if you provided more info on just exactly where the failure is rather then just saying I can't install the OS, but here are some suggestions:
First, the 6i is not going to work in the 8647 machine type, it is only supported in the 8649 machine type x-series 225.
Second, is the 5i card installed in slot 4? The 5i uses the integrated LSI channel so it has to be in slot 4 in order for it to function.
Third, with the 5i installed in slot 4 can you boot to the server raid manager CD and create your array? If you can create your array are you then installing the OS using serverguide or are you doing it straight from the OS CD? If you are using the OS CD are you pressing F6 in the begining when prompted to install the raid drivers?