Hi
I've managed to find an answer by going over some of the SQL Server Configuration examples and best procedures.
By adding a separate xml configuration to the package (it works with an environment variable too) I can set the connection string for the connection manager that is used for the SQL Server configuration.
That way any changes required to the ConnectionString for the configuration are done at the configuration stage as the package is loaded.
This linked gives an example, using an environment variable
31-days-of-ssis-sql-server-configuration