If you can't configure all packages on all servers from the same source for any reason (multiple domains, security policies, etc), but want to write packages so they can be deployed as widely as possible without modification, you probably want to use indirect configuration of the connection manager used for SQL configuration. Then you create an environment variable on each system with the connection string for the configuration table/view it should use, and you're done.

If you're asking how to retrofit this configuration scheme onto 100+ existing packages, I think there is a lot of manual editing in your future. Migrating packages in the future will probably be a lot easier once they are converted to this scheme.