The Radeon software is definitely getting better in terms of multi monitor support, but what I've noticed is with the last few builds, my taskbar on my Eyefinity enabled triple monitor setup always spans across all three.
In the settings it is set to display on one monitor, but when I log on to Windows, it spans across all three. The only way currently for me to amend this is when I log on, open the Radeon Settings software, then click on Display, then additional settings to bring up the old familiar interface. I don't have to click on anything on this interface, just as soon as it opens, it kicks in my single monitor taskbar preference.
I'm not overly bothered by it, more of an annoyance that was never there before.