Setting up more than one monitor can be tricky with ubuntu. I did this a while back once but I had to recently redo it.
Here’s my xorg.conf file http://docs.google.com/View?docid=ddw269zq_4kx25c
Here’s some tips
- use the proprietary drivers - you can get these from the ubuntu repositories
- use xinerama
- use xorg-edit http://www.cyskat.de/dee/progxorg.htm
- take a look at my xorg.conf file