The best way is to create a new replica per database, File/Replication/New Replica, select server, etc. If you have many databases that need to be replicated, you might consider shutting down the servers and copying files on the O/S level. You need to Compact the databases (from the Admin client) in order to give these databases the new On Disk Structure. ID-files are just files, they are not replicated by the server.
