Are the overclocking settings prompted as well when you first boot up? I'm at work so I can't test the configuration at the moment or I would. Thanks!!
No, by default it will use whatever the card is set at. If you set the config in trixx, close trixx, then start cgminer, cgminer should use the current card settings that trixx had set. Once you save the config file, it should save the adjusted clocks and not the default clocks. From then on, you don't need to use trixx. You can actually adjust all of that once cgminer is running from within its menus.
The startup routine will only ask about pool information.