Should fail2ban be the master of iptables rules? For example, should I setup my firewall rules along side the fail2ban rules, or should I have all my services configured and managed by fail2ban?
fail2ban is not a firewall rule manager. Fail2ban is a piece of software that monitors log files for "failed" attempts to login to a device. If it see too many failed attempts, it will then "ban" the source by adding their IP address to firewall rules to prevent future connections.