First, System Link doesn't apply to your setup so you can ignore that.

In Cubase, go to Devices, Device Setup and then VST Audio System and make sure that the Yamaha ASIO driver is selected.

You can then go to Devices, VST Connections and make sure that you have one stereo and two mono busses created. You will have to select the Add Buss button to create the two mono buses. Once you have one stereo and two mono busses created, make sure that they are assigned to the appropriate inputs in the Device Port column. Once the busses are created and set properly in VST Connections, they will become options to select in the inspector column in the project window when you create an mono or stereo audio track.