I usually interact with the shell, but I prefer to have the items on the desktop organized. Is there a command or a scripting interface to organize the desktop?
It's not entirely clear what your question is. However, if it is that you want to be able to "organise desktop icons" (i.e. into a grid) from the command-line then this will likely depend on what flavour and version of Ubuntu you are using, because they use different managers.