It's my understanding that you can run multiple Neo4j databases on the same instance, but they cannot run at the same time. In other words, multiple databases can exist, but they cannot be queried at the same time. I believe you create a new folder, and point the instance at that folder in the config before starting Neo4j. My development machine is on Windows, and I have the option to choose the folder Neo4j is supposed to use when firing up the database server.
I think the overall idea is that if your data is relate-able, then it should all be in the same database. Going to a whiteboard/mind map concept, what would be the relationship between the two databases that you'd want to query it? The line connecting the two databases would be the relationship between the data, and justify having all the data in one Neo4j database.