YES,
autoQoS does apply to IP phone traffic.
you may want to specifically mark packets appropriately for the SoftPhone specifically at the switch port. (L2 markings)
also, you can try the command:
'switchport priority extend trust'
this will enable the switch to trust the priority from the PC port, as this is where your SoftPhone is coming from.
NOTE: softphone marks voice at L3 only.
please see the following link for more info on softphone QoS:
http://www.cisco.com/en/US/products/sw/cscowork/ps2064/products_user_guide_chapter09186a008007ff73.html#xtocid11