I have two monitors attached to my Ubuntu desktop system. One is mounted above the second one (i.e. one up, one down). Unity draws the system panel across the top of each monitor - so the bottom monitor's panel is actually across the centre of my total display, with the other monitor above it.
The problem is that I can't drag a window from the top monitor to the bottom - it goes most of the way across, but I can't slide the the title-bar down across the central panel.
Strangely, it works fine dragging from bottom to top monitor - the title-bar crosses the panel with no problems.
I have a partial workaround by enabling Put in Compiz and setting mouse and keyboard shortcuts to switch windows to the other monitor, but it makes the system non-intuitive.
The ideal solution would be to move the lower monitor's panel to the bottom of the screen, but I don't think Unity works this way.