Newbie question:  How do I set the input for a series of audio recordings to be different, if I only have a 2 channel interface?

I am using a 2 channel interface (Apogee Duet) and I can record a voice and guitar track fine.  My question is how do I record a third audio track after the fact?  It seems when I attempt to record an additional track, say bass for example, Logic treats it as though it is on input 1 or 2 (which hardware wise it is of course) and merges them in a sense.   I don't know how to make it a seperate independant track, despite the fact that it was recorded through an input that I also used to record something else on a diferent track.
Thanks in advance, I very much appreciate any help.

Thanks for the response.  I know it sounds ridiculously basic.  Yes I am creating a new track and selecting it.  The third track appears in the arrange window, but changes to, for example, the third track affect the 1st.  Doesn't matter if it's a 1/4 inch guitar or XLR mic.  Yes I'm listening to the headphone output from the Duet.
I think the fundamental problem is my not understanding something about mono/stereo, or prehaps input and output settings.  I just can't seem to find the appropriate controls/settings.

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