So it defaultly boots up with 2 screens after you played with it in windows?
Strange, that means it changes something in the videobios.
To set up "twinview" (now marketted as nview) you need to be in the XF86Config(-4) file. Check the file /usr/share/doc/NVIDIA_GLX-1.0/README and the XF86Config file in that dir for more info. First read those files on how to set it up, it is not that easy to explain with all options for it.