There's a command '/nui console {mode}' where mode can be "on", "off" or "mouseover" -- '/nui console off' causes the upper console to be permanently hidden while '/nui console mouseover' will cause it to only appear when you move your mouse over the console area.
There are also several optional dashboard skins that allow you to have a transparent top console. You can find those in the "Art" section of nUI's download area at
http://www.wowinterface.com/downloads/cat125.html