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The documentation @Brendan Patterson mentions is good for customising the default theme, but if you want to customise one of the other themes, you'll have to modify that theme's JAR file.
Actually it's this somewhat buried comment that you need, to modify a bundled plugin. From Plugin loading strategies in Confluence:
Bundled plugins are included in a zip of jars called atlassian-bundled-plugins.zip which is on the main Confluence classpath, in a resources directory - <tt><confluence-install>/confluence/WEB-INF/classes/com/atlassian/confluence/setup</tt>. At Confluence startup, they are extracted and copied into the $CONFLUENCE_HOME/bundled-plugins directory, from whence they are loaded. To remove a bundled plugin (you shouldn't normally have to do this), remove the plugin from the atlassian-bundled-plugins.zip file and the bundled-plugins directory, otherwise Confluence will just put it back in place on the next startup.
So, if you want to modify something in a bundled theme that's not the default theme, you can extract the correct bundled theme from atlassian-bundled-plugins.zip, rezip the folder, then restart Confluence.
The Confluence docs cover this pretty well:
Modifying Look and Feel (for themes)
Here's how you can define a new look and feel for Confluence in your theme:
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