I've had problems using a multi-monitor setup on a native installation of Ubuntu using Gnome, namely – when I set up my laptop to be left of my main 23" monitor, I have them aligned so that the bottom edges of the monitors line up.
There are two problems with this setup:
(unrelated issue) I have been unable to successfully set a hotplugging solution that would sanely react to unplugging the main monitor from the DisplayPort and switch over to the laptop's display.
When the laptop monitor is aligned bottom in relation to the main (bigger) display to the right of it, new files, folder and shortcuts created on the desktop are positioned at the top left extremity of the rectangular bound that fits both monitors, essentially creating a "ghost" rectangular part above the laptop display that I cannot see but can interact with. The mouse can travel through this area and so can windows and other X elements.
Is there a way to enforce hard bounds around the individual displays in a multi-monitor setup like this? Ideally, I'd like it to behave the way desktop elements are handled in Windows and OSX.