I have bought 2xLCD 3D glasses Video Eyewear EVG920D 640x480 which can be connected to pc via usb and VGA. Manual says that 3D mode supported in interlaced format. I think 3D works in fullscreen mode in 640x480i or 320x200i.
Question is how to setup via command line and from C++/C# second video output as Screen :1(or whatever),set video mode(only to this display) and pass some application output to it?

Your question is not very clear. Are your display configured to run 3D? It's not automatic as far as I know. Are your glasses active or passive? You are looking for a way to display half of the vertical line every frame? Have you looked at doing this on the applications you want to display instead of X, because I don't think it is X job to handle that.

They have special mode switch 2D/3D.
Display = 3D Glasses.
3D glasses have own builtin LCD display with 640x480 resolution(aka Human Mounted Display).
In general i wish to
1) setup 640x480 videocard output2 as screen 2 (not as part of virtual resolution!)
2) pass some application output to it.
3) interlaced mode? - i dunno but maybe i need to pass 2 images(one slightly shifted) line-over-line to output valid 3d frame format.

I am not quite sure to understand what your are asking exactly (just "how can I get it to work" is not a question, I need much, much more details for that and readeaing the manual and spec, something that I will not do).

To display an application of the second screen, from the command line, write
With the right permissions, it will work. Sometime it work better if it is not done from X (ctrl+alt+f2), but it is just a permission problem. It is not the X job to handle the 3D, you will have to find out how the device work and implement the algorithm yourself.

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i managed to configure screen:0 and screen:1 with xrandr.
what i need for tests in command line is analogue to this pseudo-code
var display=system.display{2} //tryed C# mono opentk but it fail to work correctly
display.setGraphicsMode=GraphicsMode.640x480_fullscreen; //i really need this
display.setGraphicsModeFrequency=Frequency.60hz
var applicationstdout=system.exec('3dapp'); // SOLVED by DISPLAY=:1
applicationstdout.output=display; // SOLVED by DISPLAY=:1

well it's X job to display images generated in 3d 3D and frame format for device is my headache

Thnx for help Elv13