This information was provided by the awesome chm !
Check out this whitepaper on: http://www.amd.com/us/Documents/HD3D_Whitepaper.pdf It explains the different stereo 3D types that exist.
To do stereo 3D you can either use a monitor/TV that can handle stereo 3D directly through e.g. HDMI 1.4 or DP 1.2 or you can use a monitor that simply supports a high refresh rate (120Hz) and use active glasses that are synced by the GPU. In this case you will need to connect the glasses to the Vesa 3Pin connector on the FirePro board.
From a SW point of view you need just to render into an OpenGL Quadbuffer. Depending on the stereo settings you have chosen in CCC the driver will generate the appropriate format. E.g. If you chose to have interleaved stereo in CCC, your app still renders in the Quadbuffer and the driver will generate the interleaved image and send it to the display.
The same is true for HDMI 1.4. The app renders into a Quadbuffer and the driver generates the appropriate signal. Note this is only supported in full screen mode.