In the new version of the connector (written in python as opposed to ruby), there is a new required 'Project' key under the 'AgileCentral' section of the sample configuration file.
The connector is workspace scoped, so any project in the workspace will be available to the connector. The project is only used for validating the users credentials in Agile Central. So one config could cover all projects in a workspace. As long as the userid in the connector has access to edit all projects in the workspace, the connector will update any artifacts in the workspace. Also, a changeset can be associated with multiple artifacts.