I might be misunderstanding this, but have you configured your package configurations in SSIS to connect to SSIS directly?
To use package configurations successfully, you will need to set a connection to the SQL server via:
- an environment variable
- an xml file
or a registry entry.
I think it's pretty common to use an XML configuration file.
Once you have this configured, you can setup you other package configurations using a configuration table in your SQL server db that you defined in the XML file.
MCITP: Business Intelligence Developer (2005)