Nothing that I've seen as of yet. What is your purpose for running eyefinity with only 2 monitors?
The best way to set it up might be to run without eyefinity and just use windows extended desktop or something like that (i probably have the wrong name in mind) and set your main display in windows and that should be the monitor that it pops up in the middle of.
I'm sure there is a way by modifying the windows registry, but I try to stay away from those mods since if you mod the wrong thing you might be reinstalling windows.
I can state that if you pick up a 3rd monitor, and even if you go really cheap with it, that eyefinity might benefit you better and all the pop ups will come up in the center monitor.