In order to backup your PhPeace installation, you should make sure that both your database and application files are regularly backed up.
MySQL backup can be executed with the command line tool mysqldump.
A typical backup command would be
Depending on your requirements, you may want to introduce binary logging in MySQL in order to keep a copy of SQL statements between scheduled backups.
All uploaded files are stored in the uploads directory under your PhPeace installation.
Therefore, strictly speaking, all you need to backup is the configuration file (custom/config.php) and the uploads directory, and of course this can be done in different way (full, incremental, differential) depending on your backup strategy.
However, it is suggested to backup the whole installation directory. Although they can be reinstalled, application files don't add too much weight to the overall backup size and restoring the system can be much easier this way.