How do I program a stereo-capable graphics card to display stereo images?

Question

I'd like to write my own stereo image viewer, because there are certain features I need which are missing from the one bundled with my NVidia/EVGA GTX 580.

I can't figure out how to program the card to enter "shutterglass" mode where every other frame (at 120 HZ) alternates left and right.

I've looked at the OpenGL, Direct3D, and XNA APIs, as well as information from NVIDIA, and can't figure out how to get started. How do I set separate left and right images, how do I tell the screen to display it, and how to I tell the driver to activate the shutterglass transmitter?

(Another disconcerting thing is that whenever I use the bundled software to view stereo images and video in shutterglass mode, it's in fullscreen, and the screen blinks when entering that mode--even though I run the screen at 120Hz in 2D. Is there a way to have a 3D surface in a window without upsetting the rest of the screen on the NVidia "gamer" cards that are 3D capable (570, 580)?