Internal key storage uses the CryptoServer itself as the key storage medium. The keys are stored in the file CXIKEY.db, which can be seen via csadm ListFiles. The csadm BackupDatabase command is used to make an encrypted copy of the data in this file, locally, on the host where the csadm command was issued.
The csadm BackupDatabase command can be used for most database (.db) files on the CryptoServer - it will not make backups of the MBK database, for example. It can and should be used also for private database files, if you have custom modules, written using the various SDKs, which may create them.
There are additional methods for backing up .db files that csadm BackupDatabase cannot target. The MBK database, for example, must be populated from what is effectively the backup artifacts (cf csadm help=MBKImportKey). The original smartcards or keyfiles - or backups of them - that were provided to the CryptoServer in order to create the MBK internally are what you are using for the backups.