MSI Afterburner allows you to select each card, and make changes to that particular card independent of other card's settings.
I'm running a 5850 and 5830 on Win 7 64 bit and have no problems setting each card independently.
You will need either a dummy plug, run both cards in crossfire, or connect both cards to a monitor in order for Windows to recognize each card as active. On my particular miner with this setup, I have one monitor with both VGA and DVI inputs, and just have each card going to each input.
Hope that helps.