Hi,
You can add the flash intro to some page under the root document. Then, in Site Manager -> Settings -> select your site from upper left drop down -> Web site -> Default alias path and in this field set the path to the intro page, e.g.: /intro

Another option is to set the URL redirection on the root document to the intro page. This could be done in CMS Desk -> select root -> Properties -> Menu -> URL redirection.

The first approach is recommended.

Best regards,
Juraj Ondrus