It depends if your theme uses the default “searchform.php” method to override it's search bar. The plugin offers a feature to automatically replace the theme search, but not all the themes support that. The custom CSS box does nothing in this case, as it's only used to apply styling rules, but not script codes.
If the theme does not support automatic replacement, then the only possible option is to replace it manually via it's code. While this is not part of the support process, I usually try to help if I can. So if you can update your ticket with temporary FTP details, I can check to see if I can find the theme file which outputs the search bar and replace it directly.
In this case, please make sure to have a back-up of your site and database.
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