Phraseanet uses MySQL as database and stores documents n the filesystem. Backups should take care of both data stores, and application sources.
These datas are saved in directories you probably defined during setup.
An incremental backup is recommended.
ApplicationBox and DataBoxes are MySQL databases related to a Phraseanet install.
Live backups should work.
Konsole Kommander has a command to backup your DBs:
php bin/console system:backup-db /path/to/DBBackupDirectory/
This command can be included in a backup script.
Applciation sources are genrally only modified when updating Phraseanet.
It can nevertheless be good to save at one time the sources after install and setup.
You can setup your application in maintenance mode to prevent user from login and display an alert message on the frontpage. This configuration has to be done in the config.yml file. Please refer to the admin manual.