grouping ckeditor buttons in wysiwyg 6.x-2.x-dev

How does it work?

When I install ckeditor (3.1) without drupal i get an editor with grouped and draggable buttons in the editor's chrome.
When I install ckeditor with wysiwyg 6.x-2.x-dev, I get all available buttons, grouped but not draggable in the editor's chrome.
When I set specific buttons through the wysiwyg module's wysiwyg profile settings, i get an unbroken group of buttons in the editor's chrome.

My primary goal is to adjust ckeditor's chrome. Can I simply stay away from wysiwyg's profile settings and feed my adjusted setup in by changing the .js supplied by ckeditor?
My secondary goal is to figure out how wysiwyg is overriding the settings. Do you know of good documentation?