The EBS configuration only resolves to one "Endeca URL". Depending on the need of your "second Endeca instance", you could do a couple of things. If it is performance or data volume related, chances are that you need more "room" for the Endeca Server. In this case, I would move Endeca Studio to its own server and then introduce a second Endeca Server with new data domains with a load balance in front of the now two Endeca Servers.
What is the reasoning behind two Endeca instances, before we go too much farther solutioning?
You can check out the Branchbird blog for more specifics around the EBS-Endeca integration itself: