Post what is your datasource configuration (deployment) file of datasource (*-ds.xml). It has to contain definition for two databases or you must have separate datasource configuration file for each database. Then in your JBoss deployment descriptor file you're able to define for each EJB which datasource should be used for that particular EJB or you can define general datasource for all EJBs. (Of course you can define one global datasource for all of your EJBs in application but override datasource pointer just for some of EJB's).
I wouldn't touch standardjbosscmp-jdbc.xml because it is application server's configuration file and not your application configuration file. Changing server configuration file actually means that your loose your portability in some way. Deployment of your application on another JBoss server expects the change of its configuration file too.