You can try the example detailed out in this post: http://www.pixelclever.com/how-set-up-drush-for-multisite-installation which basically requires you to create a drushrc.php
file for each multisite, which includes the path to the respective modules folder.
Here are the lines from that post that explain
To start, go to your drush folder where you will find a file entitled example.drushrc.php. Copy that file into the individual site folder in your Drupal multisite installation (sites/yourmultisite), and rename the file to drushrc.php.
Now open that file and add the following line: $command_specific['dl']['destination'] = 'sites/yourmultisite/modules';
or
$command_specific['dl']['destination'] = 'sites/yourmultisite/modules/contributions';
This is also a step by step walkthrough of the updating process using drush on multisites.
http://rinen.net/2013/02/updating-a-drupal-multisite-using-drush/