The best way is to use different database groups. If you want to keep using the master database as usual ($this->db) just turn off persistent connexion configuration option to your secondary database(s). Only master database should work with persistent connexion :
Master database
$db['default']['hostname'] = "localhost";
$db['default']['username'] = "root";
$db['default']['password'] = "";
$db['default']['database'] = "database_name";
$db['default']['dbdriver'] = "mysql";
$db['default']['dbprefix'] = "";
$db['default']['pconnect'] = TRUE;
$db['default']['db_debug'] = FALSE;
$db['default']['cache_on'] = FALSE;
$db['default']['cachedir'] = "";
$db['default']['char_set'] = "utf8";
$db['default']['dbcollat'] = "utf8_general_ci";
$db['default']['swap_pre'] = "";
$db['default']['autoinit'] = TRUE;
$db['default']['stricton'] = FALSE;
Secondary database (notice pconnect is set to false)
$db['otherdb']['hostname'] = "localhost";
$db['otherdb']['username'] = "root";
$db['otherdb']['password'] = "";
$db['otherdb']['database'] = "other_database_name";
$db['otherdb']['dbdriver'] = "mysql";
$db['otherdb']['dbprefix'] = "";
$db['otherdb']['pconnect'] = FALSE;
$db['otherdb']['db_debug'] = FALSE;
$db['otherdb']['cache_on'] = FALSE;
$db['otherdb']['cachedir'] = "";
$db['otherdb']['char_set'] = "utf8";
$db['otherdb']['dbcollat'] = "utf8_general_ci";
$db['otherdb']['swap_pre'] = "";
$db['otherdb']['autoinit'] = TRUE;
$db['otherdb']['stricton'] = FALSE;
Then you can use secondary databases as database objects while using master database as usual :
// use master dataabse
$users = $this->db->get('users');
// connect to secondary database
$otherdb = $this->load->database('otherdb', TRUE);
$stuff = $otherdb->get('struff');
$otherdb->insert_batch('users', $users->result_array());
// keep using master database as usual, for example insert stuff from other database
$this->db->insert_batch('stuff', $stuff->result_array());
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