I've got that exact configuration and it doesn't work at all I'm afraid.  At least not with 64-bit Windows 7 and Catalyst 11.3 or Catalyst 11.4 (beta), and the 2.4 Stream SDK.

What happens is that if you have both cards enabled in Windows (i.e. with monitors connected, and your desktop expanded onto them), any OpenCL program you try to launch will simply freeze when it tries to initialize the OpenCL subsystem.

If you disable the 5970, then you are able to start OpenCL programs but they can only see the 6990.  AMD says they know about the problem and are "looking into it" but I'm not hopeful for a resolution anytime soon.

The 6990 is also frankly a bit annoying for everyday use, because if a program is using the first GPU for OpenCL calculations and you watch a video (YouTube, Windows Media Player, etc.) the video driver freezes and you have to reboot. This is also a "known issue," although I'm more hopeful for this one to be fixed.

But as far as the two cards working together ... I wouldn't hold out hope.  If you can figure out a way to make it work, I'd love to know how you did it.  :-)