If you are restoring on the same location you backed up from using the integrated restoration (Professional version only) you need to create a symlink in your public folder for the installation directory in your Joomla installation folder. This is done automatically by Akeeba Backup whenever you take a backup or visit its backend pages. If you need to do it manually, you will have to do something similar to this:

# Go to your PUBLIC folder
cd /var/www/html
# Create a symlink to your JOOMLA INSTALLATION folder
ln -s /opt/joomla/installation

You can then use the integrated restoration.

If you are restoring on a different location, or server (as long as it is NOT running on Windows), or if you are using Kickstart instead of the integrated restoration you need to create a symlink in your public folder for the installation directory and Akeeba Kickstart (kickstart.php) in the folder where your backup will be extracted in:

# Go to your PUBLIC folder
cd /var/www/html
# Create the symlinks to the folder you will be RESTORING YOUR SITE IN:
ln -s /opt/joomla/installation
ln -s /opt/joomla/kickstart.php

Then, upload both Akeeba Kickstart (kickstart.php) and your backup archive file(s) into the directory where you are extarcting the site into (NOT the public folder!). In the example above, this means that you need to put kickstart.php and your backup archive files into the /opt/joomla directory.

You can then run Kickstart normally.

In all cases you will have an additional restoration step, called Public Folder.

If you are restoring on the same location you backed up from you will have no option but to proceed with the same custom folder.

If you are restoring to a different location, or server, than the one you backed up from you will be shown with the automatically detected new public folder. If it's wrong (because some server configuration cannot report this folder accurately, unfortunately) you can edit it before clicking Next.

This step will move the files extracted into external_files/JPATH_PUBLIC into the (new) public folder. Any symlinks in there will be relocated so they point correctly to where your site files where extracted into. Some Joomla configuration files, as well as your .htaccess, web.config, and nginx.conf files which store the path to the Joomla installation and/or the public folder will be automatically edited to contain the new locations of your Joomla installation and/or public folder as needed.

If you are restoring on Windows you will be told that the custom installation folder is unsupported. If you continue, your site will be converted to a configuration that does NOT have a custom installation folder. However, in this case, you're better off doing what the next documentation section describes.