When you drag and drop a folder with nautilus, you must carefully set both windows on non overlapping areas of your screen, otherwise selecting one folder will bring the windows to the front, hiding the second one.
On Windows, doing so will stick the explorer.exe windows to the back and let you drag and drop the folder. I suppose it detect a long click to decide whether or not bring the window to the front.
Is that possible with Ubuntu?
Now I know that Nautilus now has split panels by pressing F3, but that not handy. Most of the time, you open a folder, THEN decide to copy. With split panel, you must decide, THEN split the panel and go to the right folder.