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Doesn't matter. AE uses system RAM, not video RAM for previews. In any case, priority of the cards is defined by your BIOS settings for your PCI stuff and the graphics driver, so this needs to be changed from the outside, if ever.
RAM for RAM Previews- yes, but what about when you want to leverage your GPU via OpenGL? I also have 2 video cards in my MacPro and AfterEffects CS5 seems to like the slower nVidia GT120 versus the effortlessly superior ATi Radeon HD 5870. I would like to be able to specify which card to use for OpenGL effects acceleration. In the case of Photoshop CS4 there was once a plug-in available to allow support for "old GPUs" or in my case just a different supported card than what the app wanted by default.
Have you tried submitting a feature request? It seems like being able to select whichever gfx card you have installed (regardless of OS) may be a cool feature in the prefs to have in future versions of AE.
Regarding video RAM: There is some benefit in giving the OpenGL renderer more texture memory (if you're using the OpenGL renderer at all, that is).
from "Render with OpenGL":
"To modify the amount of texture memory, choose Edit > Preferences > Previews (Windows) or After Effects > Preferences > Previews (Mac OS), click OpenGL Info, and enter a value for Texture Memory of no more than 80% of the installed video RAM (VRAM) on your video card."
The default is set way too low for modern cards, which have so much more memory.
But, all that said, the OpenGL renderer isn't really worth giving much thought to in After Effects. I only ever use it for the OpenGL - Interactive previews.