The Border Router setup guide spells out how to connect a USB-based network coprocessor. As I understand it, it is easy to use a serial connection of the host to connect to an NCP. Is it just a matter of changing the configuration of wpantund?
Configurating wpantund for serial communication is all done through the Config:NCP:SocketPath option. The NCP connection in the USB-based example is presented as a standard linux tty device. If your specific NCP configuration also presents the connection as a tty device, then you likely just need to change the /dev/tty* path.
If you are planning to use an SPI connection, take a look at spi-hdlc-adapter, which allows using the SPI connection as if it were a serial stream.