All of the xtrabackup configuration is done through options, which behave exactly like standard MySQL program options: they can be specified either at the command-line, or through a file such as /etc/my.cnf.
The xtrabackup binary reads the [mysqld] and [xtrabackup] sections from any configuration files, in that order. That is so that it can read its options from your existing MySQL installation, such as the datadir or some of the InnoDB options. If you want to override these, just specify them in the [xtrabackup] section, and because it is read later, it will take precedence.
You don’t need to put any configuration in your my.cnf if you don’t want to. You can simply specify the options on the command-line. Normally, the only thing you might find convenient to place in the [xtrabackup] section of your my.cnf file is the target_dir option to default the directory in which the backups will be placed, for example,
[xtrabackup] target_dir = /data/backups/mysql/
This manual will assume that you do not have any file-based configuration for xtrabackup, so it will always show command-line options being used explicitly. Please see the option and variable reference for details on all of the configuration options.
The xtrabackup binary does not accept exactly the same syntax in the my.cnf file as the mysqld server binary does. For historical reasons, the mysqld server binary accepts parameters with a --set-variable=<variable>=<value> syntax, which xtrabackup does not understand. If your my.cnf file has such configuration directives, you should rewrite them in the --variable=value syntax.
The xtrabackup tool requires no special configuration on most systems. However, the storage where the --target-dir is located must behave properly when fsync() is called. In particular, we have noticed that NFS volumes not mounted with the sync option might not really sync the data. As a result, if you back up to an NFS volume mounted with the async option, and then try to prepare the backup from a different server that also mounts that volume, the data might appear to be corrupt. You can use the sync mount option to avoid this problem.