You could try to export a full, uncompressed quicktime from the Avid but that gets to be time consuming and the files can get quite large depending on what you are doing. What I have done in the past is use the quicktime reference as a reference only and rendering out my composite with the alpha channel to re-import back to the Avid, but again that really depends on what you are doing with the footage. I would highly recommend getting the Automatic duck plug-in. It really does speed up AE projects when working with the Avid.