In SiteBuilder for Windows 3.2 you can't do it using web-interface. Custom header image just replaces some default template image. But if you need to insert flash slideshow as site header, you'll need to change template's html code.
In SiteBuilder for Windows 4.0 any user will have ability to upload own design template on Design Step in Wizard. Using such feature you will have ability to create your own, very special design.