The Librarian software uses SysEx to communicate. This requires both the MIDI In and MIDI Out to be connected, so the Atmegatron can "handshake" with the Librarian.
Although technically possible, it would be very difficult to transfer either User Waves or Memory Banks to anything other than the Librarian. However transferring single patches is easy.
To transfer a patch from the Atmegatron to your DAW: set the MIDI track in the DAW recording, or if it has a special SysEx editor, set it to receive. Then select Amplitude Attack on the Atmegatron and press and hold the function knob for at least 2 seconds. Your DAW should receive the Sysex Data.
To transfer a patch from your DAW to the Atmegatron: Select Amplitude Decay on the Atmegatron and press the function knob, so it goes green. Then either play the MIDI track in your DAW or press transmit if it has a special SysEx Editor. Your Atmegatron will receive and load the patch.