You have to convert to .tif first with Enfuse. I've used everything for this, but Irfanview is an easy option that works well out of the box. After you convert to .tif, you can then process the .tifs with Enfuse. I'm not sure if Enfuse GUI can do multiple brackets at once, but I don't think so. Photomatix can convert multiple brackets in one operation directly from .cr2 files.
Personally, I coded a massive VB script to do everything including a first stage of color adjustments and keystoning, so I just have some final tweaks to do manually. This took months.
Personally, I coded a massive VB script to do everything including a first stage of color adjustments and keystoning, so I just have some final tweaks to do manually. This took months.