You're welcome, and no. In that situation, only the amp section would be used. Feeding the D6 an analog signal using the Aux In/Out jack effectively bypasses the internal DAC. This is considered inferior to feeding a digital signal via the USB port because the DAC used by the player/source sending the signal would likely be of lower quality than the internal DACs of the D6, which are consider good.
Only use the "Phone" jack for headphones. Never use the "Aux In/Out" jack for headphones.
For the highest quality playback through the D6, play FLAC, ALAC or WMA Lossless files via the USB port. That way, you use the D6 internal DAC to convert the digital signal, and you are playing the highest quality source files through the D6. MP3 files are encoded using a "lossy" compression method, which is considered lower in quality.
In summary, for the highest quality playback, use FLAC, ALAC or WMA Lossless files via the USB port.