If you don't check the box "Replace the predefined base theme template?", it will just append what you enter to the bottom of the existing file. You can take a look at the css file that is actually generated at http://[your site]/App_Themes/[your site short name]/Default.css . There are two body sections in the css file. Browsers merge these two and the latter one will replace the prior one if they are specifying the same style.
If you do want to start from fresh, you can check the box "Replace the predefined base theme template?". It will just use whatever you enter below. There are a lot of styles that are required to render the site successfully. I would suggest you download the original one and paste there. And then start changing the style.
DotShoppingCart Staff
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