You can customize the webhelp output through the webhelp skin builder. This is an external resource that allows you to create a custom stylesheet that you can then specify in your transform. It works pretty slick.
To access the webhelp skin builder, go to http://www.oxygenxml.com/webhelp-skin-builder/. Select DITA, select a basic template to begin with, and then start customizing it. Download the CSS file to your computer.
In Oxygen, when you configure your transformation scenario, duplicate the existing webhelp option, and then edit it. On the Skins tab, select your custom CSS file.
You can add further customizations to this skin by simply adding the CSS styles in the stylesheet.
If you want to actually customize the webhelp output for the default webhelp (and apply it to all webhelp outputs), you can do so by modifying the stylesheet located here: /Applications/oxygenAuthor/frameworks/dita/DITA-OT/plugins/com.oxygenxml.webhelp/oxygen-webhelp/resources. Modify the webhelp_topic.css stylesheet.
You should also be able to add a custom stylesheet through the Parameters tab on the transformation scenario. In the args.css parameter, specify a file.
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