I've got two 560ti's in SLI. My Zotac AMP! Edition is clocked at 950Mhz and my MSI Twin Frozr II is clocked at 880Mhz. I have the MSI card as my primary because I didn't want the already toasty Zoctac to take in a little more heat from the MSI card. Now, do I have to down clock the Zotac to 880Mhz to match the other or does SLI do this automatically for the slower GPU? I've been runing SLI for a couple of days now and everything seems fine but MSI Afterburner indicates that the Zotac card is still at 950Mhz?
Yes the Zotac card will automatically run at the speed of the lower clocked MSI card to match it , so it will run without any problems.
You may tho overclock the cards together using MSI Afterburner but make sure they sync clocks when you are doing so to match each other again.
You can certainly run them with different clock speeds, but it is not ideal. When I had a similar setup I linked them via settings in MSI Afterburner on the 'General' tab. In my case the two cards were only about 20-30Mhz apart so I just overclocked them both to around 900-915Mhz. It is probably recommended that you synchronize them.