How do I make sure that the D3 DAC is set to 24-bit/96KHz audio?

If using a Mac, open the Audio MIDI Setup utility in Applications->Utilities, choose "Audioengine D3" under audio devices and check that the format is set to 96 and the bit depth is set to 24bit. Also a quick check is to simply observe the HD indicator on the D3 while music is playing. If the data rate of the digital signal being sent to the D3 is above 48K, then the HD indicator will be lit.