You should use the Adapter template set.
And at runtime you can set the ConnectionString property of each DataAccessAdapter object you use, this will be used instead of the one in the config file.
Also if both of these database reside in the same database instance, but with different catalog names.
Then you will need to use a sqlServerCatalogNameOverwrites section in your application config file, and set the new catalog name to an empty string "".
This way the catalogName passed in the connectionString will be the one to use.