What do you mean the dock is "on the top".
On the top of what?
I changed the dock preference to use the 2D style, but that's about it. It does the same thing with the bookmark submenus at the top of the bookmark menu, not just near the dock.
One thing I don't like about the overlapping sub menu is it makes it hard to access a folder that is being overlapped. If a submenu overlaps the main menu, I can no longer move the mouse down the main menu to look at other subfolders, it kind of get stuck until I escape out of the menu and then pull it down again. Does that make sense?