Hey, Lee, thanks so much for responding to my question.
I'm talking about changing things like typeface, font, size, color, column widths, height of header, footer, indentation, etc.
For example, I use the Thesis theme for my blog. Thesis has a section where you can set values for many of the styles in the site. They also have a separate css template for the user that overrides the main templates. I can make any changes in that separate css file and it's never overwritten by Thesis. I believe they accomplish this by placing a second wrapper around the whole site for a specific class, and then you modify the styles in that class. (Something like that. I'm not a programmer.)
The whole idea is to design a site I like, dictating color and style, and have all those changes remain after core updates.