The bridge for VirtueMart is used to create a bridge between JMS and VirtueMart to process the billable website creation functionalities.
It is not used to create bridge between 2 VM websites.
See the tutorial video 14 that show the case of "billable website creation" from the front-end.
www.jms2win.com/en/tutorial#jms12x-14
You don't need the JMS "bridge for VirtueMart" to process the PayPal IPN notification.
You just have to use the same "Paypal email account" for both websites.
In VM 1.X, the Paypal Payment method share the same configuration.
So you will just have to setup the "payapal payment method" with the paypal email account and the notification will be sent to the appropriate website by paypal and the notification will be processed on the correct slave site.