I'm still not entirely clear about how you have managed this, or exactly what you are recording from, come to that - it sounds like more than just the Mackie. But, if you connect a sound device to a USB input on your laptop, and select that as the device Audition uses (in Preferences>Hardware), then you physically can't record from any other source; Audition will only use that one. I suppose that if you have a USB device that can provide an output to the Windows Mixer, and you are using that as your source, you could record an internal mic as well - but only if you've selected a 'what you hear' input. If this is the case, then open the Windows Mixer record section, and select just the input you want as a source.
What should happen with the Mackie though is that it should appear as a device on its own in Audition's hardware section, and you should be selecting it from there.