What is the meaning of "channels" in an audio recorder program?
I am not sure about that particular software, but a channel is one of two sides of a stereo recording, and yes, a truly stereo microphone is in reality two separate microphones in one device.
Another option is to use two monoaural microphones connected to the same input device.

When a studio recording is being edited, a channel can represent this same; one of two microphones. There can be an even greater number of them, for example, a recording of an orchestra or they can be recordings from the same microphone made on different moments, for example, a solo artist that is recording his own chorus.