Yep that sounds like the horror that is Nvidia-Optimus. There's some kludges out there to do it all on the internal display, i don't know how well it works for mixing the two. I assume you've already looked at Bumblebee to see if it might help your situation?
Bumblebee works if you actually want to use the internal and external at the same time, but I only ever use one or the other. Also, you lose 3d acceleration if you use it, AFAIK.
