You can change the HTML template under WP-Filebase -> Settings. To edit the stylesheet goto WP-Admin -> Tools -> WP-Filebase and click <em>Edit Stylesheet</em>.
Since Version 0.1.2.0 you can create your custom templates for individual file lists. You can manage the templates under WP-Admin -> Tools -> WP-Filebase -> Manage templates. When adding a tag to a post/page you can now select the template.