This is a bit of an open issue. The current thinking is to do the following:
* Leave CSS and SS files out of the mysite folder.
* If you want to create your own HTML, and don't want to edit the theme, then duplicate the theme and edit that.
* If you want to start from scratch, then create your own theme from scratch.
The theme files take precedence over the files in mysite because the concept was that you'll override the built-in template (in mysite) with one from a theme.
However, this isn't clearly spelled out in the documentation.
From a product development perspective, the best bet is probably to remove the .ss and .css files from the mysite folder in the installer, and to improve the documentation about how to create your own custom theme.
The mysite folder should just contain your PHP and JS code.