The audio input route is still in a very primitive state - I stopped using it when I got a MIDI keyboard (apart from tuning).
It uses the default input (chosen by a library called portaudio) and no work has been done on selecting other inputs, I'm afraid. I think, however that you are not restricted to the built-in microphone: if you plug a different microphone into the mic in 3.5mm jack it will cut out the built in mic.
Having said that, using audio in to insert pitches is only really practical if the notes are coming directly from some audio source, otherwise extraneous noises means too much time correcting spurious notes.
HTH
Richard