Thanks to all.
Unfortunatly, as it turns out, xwininfo, xdpyinfo and X11::Protocol report a single screen under xinerama (2432x1064 in my case), but this is a good start.
I think Ao's idea will work, although it could be difficult to ensure the windows maximise over the top of the task bar. I'm going to have a think about that one, largely because i've never used Perl/TK :)
Any further ideas welcome.