Yes, e17 handles multiple monitors in the only way that is logical to me and I simply don't understand why things like Gnome or KDE don't work in the same way.
For example:
With gnome on two monitors I get a workspace that spans both monitors. So I can drag windows from one monitor to another. But when I change virtual desktop, it gets changed on both monitors. That makes the second monitor rather useless.
With E17, I get a workspace that spans both monitors with addition that each monitor has its own virtual desktops. So I can drag windows from one monitor to another and when I change virtual desktop, it gets changed only on the current monitor while the other one remains where it was.
This E17 feature is so important to me that I'm willing to suffer all the other bugs E17 has in order to have a normal, productive environment.