By default Sitebuilder uses Zend_Mail() which works with PHP mail() function. If you wish to use smtp connection instead of mail() function you can configure it directly in Zend Framework which located in SB_ROOT/include/Zend/. As I know all necessary files are persist.
Unfortunately, I can not give you exactly instructions what should be modified. I can suggest you to check documentation for Zend_Mail(): http://surfchen.org/zend/framework/zend.mail.sending.html