Helpinator allows you to adapt WebHelp to your website design. There's "WebHelp" tab in the CHM/WebHelp template editor with two groups: "Header" and "Footer". There you can paste HTML code that will be shown above and below WebHelp panes.
Example can be seen in Helpinator's own WebHelp:
http://www.helpinator.com/webhelp
Adapt WebHelp to your site