You can build advanced themes that add or change CSS classes, map to specific parts of the UI, and change the structure of pages. The topics linked below describe how.
You'll need to be comfortable working with FreeMarker templates. Depending on what you do, you might also need to get a more thorough understanding on how the application is structured; editing one FTL file sometimes requires knowing how a few others work, too.
The advanced topics describe how to use the admin console to create, map, and apply themes. There are simpler ways to customize the site's UI if you're looking for simple site-wide changes. You can make basic changes to color schemes and logo through the point-and-click UI described in Making Simple UI Changes. You can also download a resource kit, then upload your changes to source files as described in Customizing UI with the Theme Resource Kit.
Note: Keep in mind that the advanced changes might require more work when it's time to upgrade your site. For example, some of the FTL files you can customize depend on libraries or other FTL files that might change with the next version. If you find that the changes you want to make might require changes to the logic or Freemarker code in the FTL files, the Jive Software professional services team can help out.