Once you have grabbed a copy of Obackup, just edit the config file with your favorite text editor to setup your environment and you're ready to run. A detailled documentation can be found in the DOCUMENTATION.md file.
You can run multiple instances of obackup scripts with different backup environments. Just create another configuration file, edit it's environment and you're ready to run concurrently.
Performing remote backups requires you to create RSA private / public key pair. Please see documentation for further information.
Performing mysql backups requires to create a mysql user with SELECT rights on all databases. Please see documentation for further information.
Performing backup with SUDO_EXEC option requires to configure sudoers file to allow some commands without password. Keep in mind that running backup as superuser might be a security risk. You should generally prefer a read only enabled user. Please see documentation for further information.
File backups can be done directly if data won't change while a backup is going on (generally true on vhosts), but backing up a snapshot of the actual data is preferable as it will stay consistent. LVM, zfs or btrfs snapshots will do fine.
Backup tasks aren't always reliable, connectivity loss, insufficient disk space, hacked computers with tons of mangas to backup... Anything can happen. Obackup will sent your a warning email for every issue it can handle.
Nevertheless, you should assure yourself that your backup tasks will get done the way you meant it. Also, a backup isn't valuable until you're sure it's restoration will be a success. Try to restore your backups to check whether everything is okay. Backups will keep file permissions and owners, but may loose ACLs if destination file system won't handle them.