AE will use the card for fast previews and conventionally OpenGL accelerated effects, but not for Raytrace 3D. Check your Preview prefs if the relevant options are enabled/ available. Also search the forum and the online help under which conditions hardware acceleration will be used or when it will be disabled.
Here's a quote from the AE System Requirements page:
The following NVIDIA GPUs are supported in After Effects CS6.
Check your card against the list.
Oh, wait. You have an AMD card. I guess you don't have to check.
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