Since the GUI of the game was not meant to be modded like this (nor in any other way, for that matter), your options are still rather limited and you might notice some oddities in certain configurations. Still, using this tool should provide you with somewhat more freedom in customizing the Control Center layout than just using the pre-defined files in the ndGUI package.
If you encounter issues with your custom generated Control Center layout (such as most of the Control Center elements not getting displayed), you need to revert to any of the default layouts by replacing the current "ControlCenter.xml" file with one of the default layouts in ndGUI (as described in the "Customization / Changing the menubar position" section of the main page).
Should something like this happen and you can recall the settings which resulted in a bad layout, please notify me about the issue in the Notum Dovvetech GUI 4.3 thread or in a PM.