Magento has a hierarchy in place for its themes, which tells the system where to look for files if multiple themes are active on different stores on your website. As an example, think about a simple Magento store setup like the one you saw earlier, as demonstrated in the following diagram:

Now, imagine that your store has a theme called newtheme installed at the store view level. The Magento theme here requests a file called styles.css in the most specific interface and package first, so if you have a custom theme enabled, Magento will look in /skin/frontend/default/newtheme first. If it's not found in these directories, Magento looks in the default interfaces next: /app/design/frontend/default/default or /skin/frontend/default/default. Next, Magento will look in the base directories: /app/design/frontend/base/default or /skin/frontend/base/default. If the specified file is not found after that, Magento will encounter a rendering error.

So, the deeper down the hierarchy tree of themes the file is, the more specific it is and the more precedence it takes over other more general files.