If the size of a window gets so large that it doesn't fit on the screen and you can't manipulate it, you can simply hold the Meta key while dragging the window in the client area. This way you can move the window up or down and resize it, if you want.
If you want windows to be able to cover the dock, you can make the dock lowerable by double clicking the first dock icon while holding the Meta key. Then, you can raise and lower the dock through the first icon, just like you do with windows.
If you want windows to be able to cover menus, you can make them lowerable just like the dock by double clicking the titlebar with the Meta key pressed.