The pager preferences dialog should support setting the size of the virtual desktop of the running window manager uses viewports rather than workspaces. There may or may not be support for this in EWMH, if not, compiz preferences should be changed directly.
Created attachment 136105 [details] A patch to support viewports when compiz is running
Fixed, provided releng moves the package over.
Verified in gnome-applets-2.16.0.1-7.fc6