All of my SSIS configurations are done via XML file, not table, so I don't know if this will help at all, but Robert Davis did an article about XML named instance configuration:

http://www.sqlservercentral.com/blogs/robert_davis/archive/2008/12/11/How-Do-I-Configure-SSIS-to-Work-With-a-Named-Instance.aspx

The syntax of ServerName\InstanceName rather than ServerName alone may still apply, I'm not certain.