In SSIS 2005 a single config source (XML or SQL Server) with many connection strings could be used to setup the connections for multiple packages even if those packages did not contain all of the connections specified in the config source. In this scenario the native package configurations would read the source and attempt to apply connection strings for all those specified in the source. In cases where the connection did not exist in the SSIS package a warning would be reported however, these warnings could be ignored by setting the ‘SupressConfigurationWarnings’ property to ‘True’ within the package. This configuration strategy worked well for me in past experience since I would only have to manage the connection strings for almost all packages within a single config location. This method however, does not work in SSIS 2008 
Below is the solution I decided on however I am not totally satisfied with it. If you are also running into this issue and have something to share please comment below. Thanks!
Variable Approach
1. Inside the package there is a variable for every connection manager that will contain it’s connection string
2. The value for these variables will be derived from a package configuration pulling from a SQL Server source
3. Connection managers all are then set by an expression assigning the value of the variable to their connection string property
Benefits
1. A warning (versus error) is thrown when there is a variable in the database not found in the package that can be ignored by updating the ‘SupressConfigurationWarnings’ property to true. This is also set by another configuration.
2. A single place to manage all connection strings for all SSIS packages
Cons
1. Extra steps are involved when adding new connection managers to a package
Below are the results from my tests using the same strategy in SSIS 2005 and SSIS 2008.
2005 Output
Warning: 0×8001F02F at Package: Cannot resolve a package path to an object in the package “.Connections[Conn2].ConnectionString”. Verify that the package path is valid.
SSIS package “Package.dtsx” starting.
SSIS package “Package.dtsx” finished: Success.
2008 Output
Error at Package: The connection “Conn2″ is not found. This error is thrown by the Connections collection when the specific connection element is not found.”