Organizing the categories in Shell is fairly simple (if clunky) using Alacarte. One trick is that it's possible to put a launcher in two places in order to be able to see a program across multiple categorizations. The issue is that this creates two .desktop file references and Shell displays both of them in the All view.

I'm of a mind (and after talking with Jon he says the same), that this is a bug as Shell should compare them in this situation and see that they are the same. It should then only display one.

As a personal note though I believe that as a fix it's backward. Rather than having two launchers/.desktop files in the first place you should only have one that would be tagged (somehow) to display in multiple places.