I use the Animation Codec to make renders, I find that it usually looks better than the Avid codec. In addition i find that when we send elements out for finishing in a Flame or Smoke machine they request that the QTs use the animation codec.
Also, we use the Automatic Duck plug in… its works most of the time. The problem is trying to intergrate it into the workflow, because we use a Unity here for storage and our After Effects workstation is not connected to that, we have to transfer media using a firewire drive… it can be a very slow process sometimes.
bv1