Yes, you can add additional JavaScript and CSS file references to the /templates/{your-template}/styleguide.html file. However, after you do so you'll need to login to your control panel and reselect your template. This will reprocess the styleguide file for Website Publisher.
More information on the template system can be found here: http://idn.interspire.com/ar....r-5-Template-Guide/Page1.html
