I also have two monitors displayed in top/bottom fashion. The top one is a Safeway register screen! I use this for all of my desktop extras, such as iTunes, Alarm Clock, email, and lots of other apps.

I also have lots of problems getting said apps up to the top of the screen, for instance, confabulator, which has tons of cool looking features, but none of them will go up top!

One fix I have found is this: Go in and rearrange my preferences so the monitors are arranged side to side. Drag any stubborn apps to the 'top' screen, and change the arrangement back. Works about 90% of the time, just don't try to move it back down or you will have to do the whole thing over again.