Минут 10 ковырялся с этим. Вот результат:
dtexec /file NewSnapshot.dtsx /set \package.connections[{ConnectionID}].InitialCatalog;SmartStax_tmp /set
\package.connections[{ConnectionID}].ConnectionString;\""Data Source=Server;Initial Catalog=Database;Provider=SQLNCLI.1;Integrated
Security=SSPI;Auto Translate=false;\"" /set \package.connections[{ConnectionID}].InitialCatalog;SmartStax /set
\package.connections[{ConnectionID}].ConnectionString;\""Data Source=Server;User ID=login;Password=password;Initial
Catalog=database;Provider=SQLNCLI.1;Auto Translate=false;"\"