The concept of JMS is to share the Joomla PHP code.
So if you want to modfiy the VM2 "order_done.php" file, you can do it and it will be shared by all the websites.
If you want to set a specific Google Analytic code in this source depending on the site ID, you can add a test to know which is the site ID runing.
You have the define "MULTISITES_ID" that contain this value.
so you can do
if ( defined( 'MULTISITES_ID')) { $site_id = MULTISITES_ID; }
else { $site_id = ':master_db:'; }
You can also use the free "Multisites Google Analytics" module available in our free download.
www.jms2win.com/en/component/docman/doc_...tes-google-analytics