By default, open application windows sit on top of the Deskbar. If you need to access the Deskbar, you have to move the windows out of the way first, or click in a remaining visible portion of the Deskbar. To change this behavior, download a copy of hey and install it in ~/config/bin. Then type into a Terminal window:

hey Deskbar set Feel of Window Deskbar to 6

Of course, this now means that the Deskbar will sometimes obscure parts of your windows… you can’t have it both ways. If you like the way this works, add it to your UserBootscript.