> How can I create Desktop shortcuts?
Magic Banana suggested using symbolic links. But properly, GNOME's version of
shortcuts is launchers. You can copy any of the launchers in the main menu
either to a panel or to the desktop by dragging and dropping it. If you need
a launcher not in the menu, you can add it there by right-clicking on the
menu button and choosing "Edit Menus".
> Is there asetting somewhere so I can I stop currently running programs from
stacking on top of each other?
I don't think there is, but whether or not that happens depends on the size
of the panel. Make it shorter by a couple pixels, and it won't do that.