Im not sure if I have understood correctly how DW handles stylesheets.
In Tools » Control Panel » Stylesheet I can chose to "
Your CSS files should be placed in the /System folder in the filemanager. Upload them using the filemanager.
The tab Stylesheet, "Name of Stylesheet", page, on the tab "Template" you are able to include your own css to extend Dynamicweb Stylesheet. In this way you can choose different CSS for different pages/areas. Then you can also mark the checkbox you mention - then Dynamicweb will only include your CSS as specified and ommit the Dynamicweb generated CSS.