For example, in extended desktop mode, have 2 processes, one captures and presents desktop 1, and the other desktop 2
having two processes will not work but you could have one process that captures and presents two desktops. You can use the wglDesktopTarget call set the desktop you want to process. E.g.:
Render Desktop1 to FBO
Render Desktop2 to FBO
When doing this you need to make sure that wglDesktopTargetAMD does not get called while the rendering or present of the previous desktop has not yet finished.