The extra databases are restored in the course of the site restoration procedure by the Akeeba Backup Installer. After going through the Joomla! database, it will proceed asking you for the connection details of each database. You will be able to see the name of the database on the top of the page so that you know which database you are restoring. As usual, the SQL dump files of each database are stored inside the installation/sql directory of the archive.
The off-site files are included in the archive in a "virtual" directory. The default name of that directory is "external_files". Once the restoration is over, you will find this directory on your restored site. In it there are a few directories and a readme file. The file tells you which source path is included in each subdirectory of the external_files directory so that you can manually move the files to their appropriate location.
Do note that if you are restoring non-Joomla! PHP application such as phpBB, Coppermine, WordPress etc you have to make sure that their configuration files reflect any changes in URLs, file locations or database connection information. Akeeba Backup will not try to change any such settings.
Nicholas K. Dionysopoulos
Lead Developer and Director
🇬🇷Greek: native 🇬🇧English: excellent 🇫🇷French: basic • 🕐 My time zone is Europe / Athens
Please keep in mind my timezone and cultural differences when reading my replies. Thank you!