AutoTheory is recognized as a VST/AU Instrument within your DAW. It does not produce any sound, but allows you to load an additional VST/AU Instrument within itself. AutoTheory can also act as a MIDI Output to other instrument tracks within DAWs that support this type of routing. An AU MIDI Effect version is also included for Logic users.
Multiple instances of AutoTheory can be used within a project. All instances sync Key, Scale and Chord selections.
If you want to record the actual MIDI being played by AutoTheory, you will need to set up a track for AutoTheory as well as the destination instrument track. You will then need to Record both tracks at the same time.
Most DAWs allow for this (Maschine and Reason excluded). Each DAW will have slightly different nuances for recording multiple tracks simultaneously, but the idea is the same.