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You don't need to modify the MAX II firmware to use the USB direct interface. There are two ways to do it:
The easy way is to instantiate an altera_usb_debug_master within your FPGA and connect its conduit interface to the pins which route to the USB direct pins on the USB-Blaster II MAX. Then use SystemConsole to read and write through this master.
The difficult way is to take apart this component and use the altera_usb_debug_fifos component within it to terminate the interface. This gets you a raw avalon streaming FIFO in each direction that you can connect to your hardware. Use the appropriate host libraries (libusb on linux or winusb on windows) to locate and open the USB device - the second set of interfaces are used for communicating with the direct endpoint. Any data sent to the USB OUT interface will appear on the fifo's avst_src interface, data from the avst_sink interface will appear on the host's USB IN interface. USB Packet boundaries are ignored for out, for in there is a ~100 clock timeout before the MAX sends an incomplete packet to the host.
I recommend getting the easy way working first even if you plan to use the difficult way later as it will get past the trivial but inevitable mistakes (pin assignments or clocks wrong etc).
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Hi i am a newbie to system console and been trying to get the commands for performing the read and write in the USB debug master component.