Either you misunderstand the question, or the OP misunderstands the capabilities of the X root window and display limitations.
Anyway, I ran like this for a long time, first with two monitors then with three. I tried several solutions and ended up writing an ugly hack for some X library which allowed me to specify viewports in a config file. Eventually that broke due to changes to multiple monitor code further upstream, so I ditched my two 17" screens and got a better videocard and a massive 24" LCD - problem solved.
I haven't experienced multiple monitors on ATI under Linux, but at least with nVidia's pathetic dedication to the platform (and insultingly stubborn tech support) it was a painful experience and I wouldn't recommend trying.