If you go to Options Menu, Advanced sub menu, and chose Make Boards Always on Top, you can set it so boards are always on top windows. If a board is over a chat console partially covering it, clicking on the chat window or typing in chat window will not bring chat window to front but keep it behind the board. Boards themselves can of course cover other boards. Another property is that when you minimize Lantern, the board is it's own window now, and won't minimize as well unless you minimize it additionally. This allows you to have a board or boards up while lantern is otherwise minimized and you can have other windows open such as your browser and other applications to for example read while watching a game.
The way this work is when you select the setting. a popup comes up saying you must restart lantern for this to take effect. Nothing will change till you shut down and reopen lantern. You can keep selecting this option turning the setting on or off till you arrive at a final decision. What it is set to when the program opens is what you get. Of course you can chang it back and restart lantern if you want the regular boards again.