I think the quickest way would be:
<?php
    Configure::load('swiftmailer');
    $this->SwiftMailer->smtpType =
      Configure::read('SwiftMailer.'.Configure::read().'.smtpType');
    $this->SwiftMailer->smtpHost = 
      Configure::read('SwiftMailer.'.Configure::read().'.smtpHost');
    $this->SwiftMailer->smtpPort = 
      Configure::read('SwiftMailer.'.Configure::read().'.smtpPort');
    $this->SwiftMailer->smtpUsername = 
      Configure::read('SwiftMailer.'.Configure::read().'.smtpUsername');
    $this->SwiftMailer->smtpPassword = 
      Configure::read('SwiftMailer.'.Configure::read().'.smtpPassword');
?>
Now where to put it on.
I would suggest the Controller constructor, that way it's nice and tidy.
For the values you can always use a private config file:
// /app/config/swiftmailer.php:
<?php
  $config['SwiftMailer'][0]['smtpType'] = 'value';
  $config['SwiftMailer'][0]['smtpHost'] = 'value';
  $config['SwiftMailer'][0]['smtpPort'] = 'value';
  $config['SwiftMailer'][0]['smtpUsername'] = 'value';
  $config['SwiftMailer'][0]['smtpPassword'] = 'value';
  $config['SwiftMailer'][1]['smtpType'] = 'value';
  $config['SwiftMailer'][1]['smtpHost'] = 'value';
  $config['SwiftMailer'][1]['smtpPort'] = 'value';
  $config['SwiftMailer'][1]['smtpUsername'] = 'value';
  $config['SwiftMailer'][1]['smtpPassword'] = 'value';
  $config['SwiftMailer'][2]['smtpType'] = 'value';
  $config['SwiftMailer'][2]['smtpHost'] = 'value';
  $config['SwiftMailer'][2]['smtpPort'] = 'value';
  $config['SwiftMailer'][2]['smtpUsername'] = 'value';
  $config['SwiftMailer'][2]['smtpPassword'] = 'value';
?>
You can find a more generic example on Configuration Class v 1.2 and Configuration Class v 1.3.
They seem to have the same content, so it seems that it hasn't changed from 1.2 to 1.3.
Hope it helps.