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Good question — I don’t know to be honest, I’d have to play around with it. I epicly loathe the way WP handles URLs — it’s one of the weakest areas of the application, and wrestling with them makes me want to scream at the developers. </rant>

You can set the permalink structure for your entire site, but you’ll have to play around with the permalink settings available for each post type (check out some of the options available when you edit your CCT definitions). My goal with all those options was to pass arguments as transparently as possible to the underlying WordPress functions, but that’s no guarantee that those underlying functions are sensible in their handling of that data.