I believe that you can use your hibernate cfg files as is (though I've never done it myself).. Handling transactions is going to be your biggest problem (imo). you can choose to handle the transactions your self or choose xa-transactions. Search for posts by me, as I've got posts about both.
I was looking at the /resources/META-INF/persistence-dev.xml file and I'm thinking maybe there's a way to work my various data sources into that file and specify them by name to the EntityManager. Is that something that's possible?