WordPress.com upgrades are only useful for WordPress.cm blogs. In fact, you can easily alter any theme file on a self-hosted WordPress.org installation, including the CSS (style.css).
You can do this from Appearance -> Editor in your blog's Dashboard, or install Jetpack and activate the Custom CSS module for a more familiar experience: http://jetpack.me/
Your Custom CSS changes can't be transferred, but if you use the Custom CSS module from Jetpack, you can simply copy and past the CSS rules from blog to blog.