I'm of the impression that this can be achieved with a 2 channel (using Red and white cables) into your PC from the noise filter? This would make sense for at least Pokemon I would presume - the sound effects are on one channel and the music is on the other?
At present I just use USB audio, but also have a ground loop isolator that is one connection to my sound card as opposed to two separate connections.
If someone could confirm this for me, would be appreciated