In Jitter you can, no problem. Just a matter of positioning 2 jit.windows correctly.
The other option is to make just 1 jit.window that spans both outputs and position the contents (2 videoplanes for example) accordingly within it. That’s what I do. Advantage is that everything can be contained within one openGL rendering context this way.
Search for my triplehead post for an elaborate example of multiscreen rendering with Jitter.
Yes and indeed to the OS the matrox and its outputs look like 1 screen, so fullscreening a window will span all outputs. But the point is that in Jitter you choose yourself where the windows go, so it’s not an issue. You don’t use the fullscreen command but give the window a specific size and position. Now if you plan to use it with other software you might wanna check if it’s gonna work the way you intend.