If you want to insert data to the database outside Java, you need to use native SQL. Use SQL Standard to make sure most databases can execute the script. When the application runs, JPA will make the mapping of the new data and convert it into objects when needed.
How to make sure the script works in all databases? Well that's the same problem any DBA has when making Store Procedures or native queries... that's why JPA exists, to avoid making it directly in SQL, but I know sometimes it's needed that way.
I suggest you to make 3 main scripts. One for Oracle, one for SQL Server (there are some issues in the date datatypes from 2005 to 2008 versions so be careful), and one for MySQL. Start your script with standard SQL and when you test it in these databases you will find some fixes you will need to do for each DBMS.
Once you got it, you can make a file script (*.sql file) and run it with the DB manager. If it works, run the server, put the app online and the data will be integrated just fine.