At first, it was a hard concept for me to grasp but, in CS6 the codec associated with a particular Sequence (Preset) is essentially ignored, it's all the other parameters that are critical (i.e Timebase/frame rate, Frame Size and Pixel Aspect Ratio). I use a AJA LHi card but I created, or more accurately re-named, most of my common presets based on the AVC-Intra (AVC-I 100) presets for HD and DVCPRO50 presets for SD. As I recall I kept most all settings untouched with the exception of one preset where I changed the Frame Size from 720x480 to 720x486 only because I could not find a preset with those settings.
If you start with one of these presets, all the critical settings are predetermined and are AJA ready. Having a setting for an AJA codec (even if they were available for CS6) would be pretty meaningless. I suppose if you could set your Preview File Format to an AJA codec, and you ALWAYS exported using preview files, you might see some efficiency. I just keep my Preview File Format set at I-Frame Only MPEG, the quality is excellent and the render files are quite small.