I run synergy with three machines. I have warcraft running on my main machine in Windowed Mode but with the Maximized option checked. This looks the same as if it is in Full Screen mode. The other two machines are running two instances of warcraft in Windowed Mode and in 1040x786. When I move my mouse out of my main display, Warcraft stays maximized but I see the blue task bar from my desktop.

So I think the answer you're looking for is to go into your video options and select Windowed Mode and Maximized. Then you can seemlessly move your mouse around your systems.