Do you mean with Nvidia's DUal View, or ATI's equivalent? I found DUal View a PITA. Managed to get it set how I want pretty much by fluke. ATI's way was much better.
If you right click and go to properties and the setting stab, you can drag the monitor to the other side...
Might help. If not, Google for UltraMon. I haven't had the need to use it yet, as I've just managed to get Dual View to work with me, but people do recommend it.