I wouldn’‘t recommend the embedded database for a setup with more than 500 users. It’‘s not that it’'s not going to work but having an external database will help you release resources needed by Wildfire itself and it will also let you use any SQL tool to manage the database in a more appropriate way.
To make the migration to MySQL you may reuse the SQL statements stored in [wildfire home]/embedded-db. There is a script file that could be used as a basis for running similar statements to populate the new database. Search in this forums for a thread about this topic.