One option is to register 2 database handles from within your bootstrap.php, one for each connection. E.g.:

$parameters = array(
                    'host'     => 'xx.xxx.xxx.xxx',
                    'username' => 'test',
                    'password' => 'test',
                    'dbname'   => 'test'
                   );
try {
    $db = Zend_Db::factory('Pdo_Mysql', $parameters);
    $db->getConnection();
} catch (Zend_Db_Adapter_Exception $e) {
    echo $e->getMessage();
    die('Could not connect to database.');
} catch (Zend_Exception $e) {
    echo $e->getMessage();
    die('Could not connect to database.');
}
Zend_Registry::set('db', $db);

$parameters = array(
                    'host'     => 'xx.xxx.xxx.xxx',
                    'username' => 'test',
                    'password' => 'test',
                    'dbname'   => 'test'
                   );
try {
    $db = Zend_Db::factory('Pdo_Mysql', $parameters);
    $db->getConnection();
} catch (Zend_Db_Adapter_Exception $e) {
    echo $e->getMessage();
    die('Could not connect to database.');
} catch (Zend_Exception $e) {
    echo $e->getMessage();
    die('Could not connect to database.');
}
Zend_Registry::set('db2', $db);

In your controllers (e.g.):

public function init()
{
     $this->db = Zend_Registry::get('db');
     $this->db2 = Zend_Registry::get('db2');
}

public function fooAction()
{
    $data = $this->db2->fetchAll('select foo from blah');
    ...
}