Not sure what's available in your version but in 5.6 you will be able to indicate your Aware IM-specific file (like blue.css) and even a javascript file if a theme requires one.
Mots probably, this is supported in your version as well. You need to create the Aware IM specific CSS file like blue2.css and then specify it in the themes.props file AFTER the main CSS file of the theme separated by semi-colon. Look at how this is done for the Clifton themes.
You need to restart Aware IM after changes to the theme.props