Hi Dee,
The cart is just a module that sits on a page with or without ssl enabled, there is no specific coding in the cart that is specific your domain name or SSL. SSL certs are installed in IIS and enabled in dnn either portal wide or by page.
If you are trying to run 2 portals using shared hosting with a shared IP and the same SSL cert you most likely will need to upgrade your hosting to a dedicated ip in order to get SSL working properly on both portals.
The following forum post may help:
http://www.smith-consulting.com/Forums/forumid/1/postid/8235/scope/posts.aspx#8235