It really depends on your software. Windows will automatically default to one of the inputs, and you can change which in control panel. However, if your software allows you to choose which input instead of using Windows default, then you can use both inputs at once. You shouldn't have to disable either of them. For example, my xbox 360 headset (plugged in the controller and then to the computer via USB) is the sound output for TeamSpeak, but my speakers are the sound output for my games. So when people talk, I hear them through the headset, but the game sound is still through my surround sound speakers. I know that is output, but input will be the same.