Hi,
QoS is bound to the hardware. Therefore queueing will be the same on a link, whether it is part of an etherchannel or not.
The only difference would be how the switch selects which physical link to select for a given frame. There are several configurable options depending on your hard- and software. An example for this is found f.e. in "Configuring EtherChannel Load Balancing"
http://www.cisco.com/en/US/products/hw/switches/ps5206/products_configuration_guide_chapter09186a008017ff88.html#33657
Hope this helps! Please rate all posts.
Regards, Martin