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work in progress document, meanwhile:

General README documentation
Per Windows Settings

The ideal solution for multiview would be to create different display profiles in the User Preference. Then the user could pick a profile (from a preset list) for the current window. The profile could include color management settings as well as stereoscopy mode (side-by-side, anaglyph, ...). That would allow the user to work in a mixed environment with a regular display (where s/he would use anaglyph) and a real stereo 3d display.

This won't happen any soon since it's been in Blender's todo for a long time. Instead I'm proposing a different approach. Basically we have an option in User Preference (as it is now) to pick the preferable 3d stereo method. Every time you open Blender this will be the method assigned to the windows. On top of that we create an operator (shortcut D+1, D+2, ..., or no shortcuts predefined) where the user can switch the 3d method for the current window.

If the method picked by the user requires 'Full Area' the 3D areas (UV Editor, 3D View) will show interlaced with an overlayed message suggesting the user to 'Fullscreen Area' (or double-click, or to use the shortcut Alt+F10).