I found a past post from someone experienced with audio sampling that may answer your question:
http://forums.ni.com/ni/board/message?board.id=170&message.id=40154
Because the M Series boards similarly use multiplexed ADCs the same concerns will apply to the PCI-6229. If you are only sampling one channel at a time, then it should be just fine. Simply perform an analog voltage measurement.
Good luck,
Jason