An app.config file can have multiple connection strings. Each must be given a unique name so that your code can specify the the appropriate one for the query. For example:
<configuration>
<connectionStrings>
<add name="Database1" connectionString="Data Source=Server1;Initial Catalog=Database1;Integrated Security=SSPI" providerName="System.Data.SqlClient" />
<add name="Database2" connectionString="Data Source=Server2;Initial Catalog=Database2;Integrated Security=SSPI" providerName="System.Data.SqlClient" />
</connectionStrings>
</configuration>