I believe what you're recommending is part of CORE-828. The idea is persistence across upgrades. You add your CSS, Javascript overrides and when you upgrade those still exist.
What I'd recommend doing in 3.2 b1 now is to edit the structure.pdt file and link your custom CSS. Then, when you upgrade you'll just have to add the link to your custom CSS back to structure.pdt. After CORE-828 is implemented, you obviously wouldn't have to do this.
Keep in mind though, all the colors can be changed under Look and Feel in the settings, admin and client themes. Creating your own color scheme is the quickest way to get up and running with something that at least matches your website. I think of there being 3 levels of customization.
1. Change the theme, or create a custom theme in Settings > Look and Feel. (Simplest)
2. Override some CSS styles (edit structure.pdt and add your custom CSS override file) (More difficult)
3. Copy the template directory, rename it and go nuts. In 3.2 b1 you can select the new templates under Look and Feel > Templates. (Most difficult)