I just went through the process of adding SSL support to my site, using a cert I bought from godaddy. Everything works fine with ISPConfig in this respect, but I ran into trouble using the SSLChainFile supplied by godaddy. ISPConfig does not support ChainFiles directly, but you can easily add support on a site by site basis by adding a reference to it in the Apache Directives textarea within the ISPConfig control panel.
First, upload the Chain file to the ssl folder of your website. Next, add a reference to it in the Apache Directives field. In my case, this was: